3.6.1 BAli-Phy estimates multiple sequence alignments and evolutionary trees. Ben Redelings Redelings, B. (2014) Erasing Errors due to Alignment Ambiguity When Estimating Positive Selection. Molecular Biology and Evolution 31, 1979-1993 Suchard, M.A. and Redelings, B.D. BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny, Bioinformatics, 22:2047-2048, 2006. Phylogeny / Alignment bali_phy3_xsede baliphy_expanse_open perl !$specify_wrapup && !$specify_mr && $which_runtype == 3 perl " bali-phy sequences.fasta" 0 baliphy_expanse_open_wrap perl $specify_wrapup && !$specify_mr && $which_runtype == 2 perl " bali-phy sequences.fasta" 0 baliphy_expanse_wayne perl $specify_wrapup && !$specify_mr && $which_runtype == 1 perl " sequences.fasta" 0 baliphy_expanse_opena perl defined $input_file2 && !$specify_mr perl "sequences2.fasta" 1 baliphy_expanse_openb perl defined $input_file3 && !$specify_mr perl "sequences3.fasta" 2 baliphy_expanse_openc perl defined $input_file4 && !$specify_mr perl "sequences4.fasta" 3 baliphy_expanse_opend perl defined $input_file5 && !$specify_mr perl "sequences5.fasta" 4 baliphy_expanse_opene perl defined $input_file6 && !$specify_mr perl "sequences6.fasta" 5 baliphy_expanse_middle perl !$specify_wrapup && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 8 baliphy_expanse_middle_wrap perl $specify_wrapup && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 8 baliphy_expanse_end perl !$specify_mr perl "-I 1:$model_type_1 --alphabet 1:$datatype -S 1:$substitution_model$gammarates41$invariable1" 9 baliphy_expanse_enda perl defined $input_file2 && !$specify_mr perl "-I 2:$model_type_2 --alphabet 2:$datatype_2 -S 2:$substitution_model2$gammarates42$invariable2" 10 baliphy_expanse_endb perl defined $input_file3 && !$specify_mr perl "-I 3:$model_type_3 --alphabet 3:$datatype_3 -S 3:$substitution_model3$gammarates43$invariable3" 14 baliphy_expanse_endc perl defined $input_file4 && !$specify_mr perl "-I 4:$model_type_4 --alphabet 4:$datatype_4 -S 4:$substitution_model4$gammarates44$invariable4" 15 baliphy_expanse_endd perl defined $input_file5 && !$specify_mr perl "-I 5:$model_type_5 --alphabet 5:$datatype_5 -S 5:$substitution_model5$gammarates45$invariable5" 16 baliphy_expanse_ende perl defined $input_file6 && !$specify_mr perl "-I 6:$model_type_6 --alphabet 6:$datatype_6 -S 6:$substitution_model6$gammarates46$invariable6" 17 baliphy_expanse_open2 perl !$specify_wrapup && $specify_multiruns > 1 && !$specify_mr perl "&& bali-phy sequences.fasta" 20 baliphy_expanse_open_wrap2 perl $specify_wrapup && $specify_multiruns > 1 && !$specify_mr perl "&& bali-phy sequences.fasta" 20 baliphy_expanse_open2a perl $specify_multiruns > 1 && defined $input_file2 && !$specify_mr perl "sequences2.fasta" 21 baliphy_expanse_open2b perl $specify_multiruns > 1 && defined $input_file3 && !$specify_mr perl "sequences3.fasta" 22 baliphy_expanse_open2c perl $specify_multiruns > 1 && defined $input_file4 && !$specify_mr perl "sequences4.fasta" 23 baliphy_expanse_open2d perl $specify_multiruns > 1 && defined $input_file5 && !$specify_mr perl "sequences5.fasta" 24 baliphy_expanse_open2e perl $specify_multiruns > 1 && defined $input_file6 && !$specify_mr perl "sequences6.fasta" 25 baliphy_expanse_middle2 perl $specify_multiruns > 1 && !$specify_wrapup && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 26 baliphy_expanse_middle_wrap2 perl $specify_wrapup && $specify_multiruns > 1 && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 26 baliphy_expanse_end2 perl $specify_multiruns > 1 && !$specify_mr perl "-I 1:$model_type_1 --alphabet 1:$datatype -S 1:$substitution_model$gammarates41$invariable1" 27 baliphy_expanse_end2a perl $specify_multiruns > 1 && defined $input_file2 && !$specify_mr perl "-I 2:$model_type_2 --alphabet 2:$datatype_2 -S 2:$substitution_model2$gammarates42$invariable2" 28 baliphy_expanse_end2b perl $specify_multiruns > 1 && defined $input_file3 && !$specify_mr perl "-I 3:$model_type_3 --alphabet 3:$datatype_3 -S 3:$substitution_model3$gammarates43$invariable3" 29 baliphy_expanse_end2c perl $specify_multiruns > 1 && defined $input_file4 && !$specify_mr perl "-I 4:$model_type_4 --alphabet 4:$datatype_4 -S 4:$substitution_model4$gammarates44$invariable4" 30 baliphy_expanse_end2d perl $specify_multiruns > 1 && defined $input_file5 && !$specify_mr perl "-I 5:$model_type_5 --alphabet 5:$datatype_5 -S 5:$substitution_model5$gammarates45$invariable5" 31 baliphy_expanse_end2e perl $specify_multiruns > 1 && defined $input_file6 && !$specify_mr perl "-I 6:$model_type_6 --alphabet 6:$datatype_6 -S 6:$substitution_model6$gammarates46$invariable6" 32 baliphy_expanse_open3 perl !$specify_wrapup && $specify_multiruns > 2 && !$specify_mr perl "&& bali-phy sequences.fasta" 40 baliphy_expanse_open_wrap3 perl $specify_wrapup && $specify_multiruns > 2 && !$specify_mr perl "& bali-phy sequences.fasta" 40 baliphy_expanse_open3a perl $specify_multiruns > 2 && defined $input_file2 && !$specify_mr perl "sequences2.fasta" 41 baliphy_expanse_open3b perl $specify_multiruns > 2 && defined $input_file3 && !$specify_mr perl "sequences3.fasta" 42 baliphy_expanse_open3c perl $specify_multiruns > 2 && defined $input_file4 && !$specify_mr perl "sequences4.fasta" 43 baliphy_expanse_open3d perl $specify_multiruns > 2 && defined $input_file5 && !$specify_mr perl "sequences5.fasta" 44 baliphy_expanse_open3e perl $specify_multiruns > 2 && defined $input_file6 && !$specify_mr perl "sequences6.fasta" 45 baliphy_expanse_middle3 perl $specify_multiruns > 2 && !$specify_wrapup && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 46 baliphy_expanse_middle_wrap3 perl $specify_wrapup && $specify_multiruns > 2 && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 46 baliphy_expanse_end3 perl $specify_multiruns > 2 && !$specify_mr perl "-I 1:$model_type_1 --alphabet 1:$datatype -S 1:$substitution_model$gammarates41$invariable1" 47 baliphy_expanse_end3a perl $specify_multiruns > 2 && defined $input_file2 && !$specify_mr perl "-I 2:$model_type_2 --alphabet 2:$datatype_2 -S 2:$substitution_model2$gammarates42$invariable2" 48 baliphy_expanse_end3b perl $specify_multiruns > 2 && defined $input_file3 && !$specify_mr perl "-I 3:$model_type_3 --alphabet 3:$datatype_3 -S 3:$substitution_model3$gammarates43$invariable3" 49 baliphy_expanse_end3c perl $specify_multiruns > 2 && defined $input_file4 && !$specify_mr perl "-I 4:$model_type_4 --alphabet 4:$datatype_4 -S 4:$substitution_model4$gammarates44$invariable4" 50 baliphy_expanse_end3d perl $specify_multiruns > 2 && defined $input_file5 && !$specify_mr perl "-I 5:$model_type_5 --alphabet 5:$datatype_5 -S 5:$substitution_model5$gammarates45$invariable5" 51 baliphy_expanse_end3e perl $specify_multiruns > 2 && defined $input_file6 && !$specify_mr perl "-I 6:$model_type_6 --alphabet 6:$datatype_6 -S 6:$substitution_model6$gammarates46$invariable6" 52 baliphy_expanse_open4 perl !$specify_wrapup && $specify_multiruns > 3 && !$specify_mr perl "&& bali-phy sequences.fasta" 60 baliphy_expanse_open_wrap4 perl $specify_wrapup && $specify_multiruns > 3 && !$specify_mr perl "& bali-phy sequences.fasta" 60 baliphy_expanse_open4a perl $specify_multiruns > 3 && defined $input_file2 && !$specify_mr perl "sequences2.fasta" 61 baliphy_expanse_open4b perl $specify_multiruns > 3 && defined $input_file3 && !$specify_mr perl "sequences3.fasta" 62 baliphy_expanse_open4c perl $specify_multiruns > 3 && defined $input_file4 && !$specify_mr perl "sequences4.fasta" 63 baliphy_expanse_open4d perl $specify_multiruns > 3 && defined $input_file5 && !$specify_mr perl "sequences5.fasta" 64 baliphy_expanse_open4e perl $specify_multiruns > 3 && defined $input_file6 && !$specify_mr perl "sequences6.fasta" 65 baliphy_expanse_middle4 perl $specify_multiruns > 3 && !$specify_wrapup && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 66 baliphy_expanse_middle_wrap4 perl $specify_wrapup && $specify_multiruns > 3 && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 66 baliphy_expanse_end4 perl $specify_multiruns > 3 && !$specify_mr perl "-I 1:$model_type_1 --alphabet 1:$datatype -S 1:$substitution_model$gammarates41$invariable1" 67 baliphy_expanse_end4a perl $specify_multiruns > 3 && defined $input_file2 && !$specify_mr perl "-I 2:$model_type_2 --alphabet 2:$datatype_2 -S 2:$substitution_model2$gammarates42$invariable2" 68 baliphy_expanse_end4b perl $specify_multiruns > 3 && defined $input_file3 && !$specify_mr perl "-I 3:$model_type_3 --alphabet 3:$datatype_3 -S 3:$substitution_model3$gammarates43$invariable3" 69 baliphy_expanse_end4c perl $specify_multiruns > 3 && defined $input_file4 && !$specify_mr perl "-I 4:$model_type_4 --alphabet 4:$datatype_4 -S 4:$substitution_model4$gammarates44$invariable4" 70 baliphy_expanse_end4d perl $specify_multiruns > 3 && defined $input_file5 && !$specify_mr perl "-I 5:$model_type_5 --alphabet 5:$datatype_5 -S 5:$substitution_model5$gammarates45$invariable5" 70 baliphy_expanse_end4e perl $specify_multiruns > 3 && defined $input_file6 && !$specify_mr perl "-I 6:$model_type_6 --alphabet 6:$datatype_6 -S 6:$substitution_model6$gammarates46$invariable6" 70 baliphy_expanse_open5 perl !$specify_wrapup && $specify_multiruns > 4 && !$specify_mr perl "&& bali-phy sequences.fasta" 78 baliphy_expanse_open_wrap5 perl $specify_wrapup && $specify_multiruns > 4 && !$specify_mr perl "& bali-phy sequences.fasta" 78 baliphy_expanse_open5a perl $specify_multiruns > 4 && defined $input_file2 && !$specify_mr perl "sequences2.fasta" 79 baliphy_expanse_open5b perl $specify_multiruns > 4 && defined $input_file3 && !$specify_mr perl "sequences3.fasta" 79 baliphy_expanse_open5c perl $specify_multiruns > 4 && defined $input_file4 && !$specify_mr perl "sequences4.fasta" 79 baliphy_expanse_open5d perl $specify_multiruns > 4 && defined $input_file5 && !$specify_mr perl "sequences5.fasta" 79 baliphy_expanse_open5e perl $specify_multiruns > 4 && defined $input_file6 && !$specify_mr perl "sequences6.fasta" 79 baliphy_expanse_middle5 perl $specify_multiruns > 4 && !$specify_wrapup && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 80 baliphy_expanse_middle_wrap5 perl $specify_wrapup && $specify_multiruns > 4 && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 80 baliphy_expanse_end5 perl $specify_multiruns > 4 && !$specify_mr perl "-I 1:$model_type_1 --alphabet 1:$datatype -S 1:$substitution_model$gammarates41$invariable1" 81 baliphy_expanse_end5a perl $specify_multiruns > 4 && defined $input_file2 && !$specify_mr perl "-I 2:$model_type_2 --alphabet 2:$datatype_2 -S 2:$substitution_model2$gammarates42$invariable2" 81 baliphy_expanse_end5b perl $specify_multiruns > 4 && defined $input_file3 && !$specify_mr perl "-I 3:$model_type_3 --alphabet 3:$datatype_3 -S 3:$substitution_model3$gammarates43$invariable3" 81 baliphy_expanse_end5c perl $specify_multiruns > 4 && defined $input_file4 && !$specify_mr perl "-I 4:$model_type_4 --alphabet 4:$datatype_4 -S 4:$substitution_model4$gammarates44$invariable4" 81 baliphy_expanse_end5d perl $specify_multiruns > 4 && defined $input_file5 && !$specify_mr perl "-I 5:$model_type_5 --alphabet 5:$datatype_5 -S 5:$substitution_model5$gammarates45$invariable5" 81 baliphy_expanse_end5e perl $specify_multiruns > 4 && defined $input_file6 && !$specify_mr perl "-I 6:$model_type_6 --alphabet 6:$datatype_6 -S 6:$substitution_model6$gammarates46$invariable6" 81 baliphy_expanse_open6 perl !$specify_wrapup && $specify_multiruns > 5 && !$specify_mr perl "&& bali-phy sequences.fasta" 86 baliphy_expanse_open_wrap6 perl $specify_wrapup && $specify_multiruns > 5 && !$specify_mr perl "& bali-phy sequences.fasta" 86 baliphy_expanse_open6a perl $specify_multiruns > 5 && defined $input_file2 && !$specify_mr perl "sequences2.fasta" 87 baliphy_expanse_open6b perl $specify_multiruns > 5 && defined $input_file3 && !$specify_mr perl "sequences3.fasta" 87 baliphy_expanse_open6c perl $specify_multiruns > 5 && defined $input_file4 && !$specify_mr perl "sequences4.fasta" 87 baliphy_expanse_open6d perl $specify_multiruns > 5 && defined $input_file5 && !$specify_mr perl "sequences5.fasta" 87 baliphy_expanse_open6e perl $specify_multiruns > 5 && defined $input_file6 && !$specify_mr perl "sequences6.fasta" 87 baliphy_expanse_middle6 perl $specify_multiruns > 5 && !$specify_wrapup && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 88 baliphy_expanse_middle_wrap6 perl $specify_wrapup && $specify_multiruns > 5 && !$specify_mr perl "-n $specify_dirname -i $num_iterations" 88 baliphy_expanse_end6 perl $specify_multiruns > 5 && !$specify_mr perl "-I 1:$model_type_1 --alphabet 1:$datatype -S 1:$substitution_model$gammarates41$invariable1" 89 baliphy_expanse_end6a perl $specify_multiruns > 5 && defined $input_file2 && !$specify_mr perl "-I 2:$model_type_2 --alphabet 2:$datatype_2 -S 2:$substitution_model2$gammarates42$invariable2" 89 baliphy_expanse_end6b perl $specify_multiruns > 5 && defined $input_file3 && !$specify_mr perl "-I 3:$model_type_3 --alphabet 3:$datatype_3 -S 3:$substitution_model3$gammarates43$invariable3" 89 baliphy_expanse_end6c perl $specify_multiruns > 5 && defined $input_file4 && !$specify_mr perl "-I 4:$model_type_4 --alphabet 4:$datatype_4 -S 4:$substitution_model4$gammarates44$invariable4" 89 baliphy_expanse_end6d perl $specify_multiruns > 5 && defined $input_file5 && !$specify_mr perl "-I 5:$model_type_5 --alphabet 5:$datatype_5 -S 5:$substitution_model5$gammarates45$invariable5" 89 baliphy_expanse_end6e perl $specify_multiruns > 5 && defined $input_file6 && !$specify_mr perl "-I 6:$model_type_6 --alphabet 6:$datatype_6 -S 6:$substitution_model6$gammarates46$invariable6" 89 number_nodes1b 2 scheduler.conf perl !$more_memory && !$specify_multirun && $which_runtype == 1 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=4G\\n" . "threads_per_process=2\\n" number_nodes1 2 scheduler.conf perl !$more_memory && !$specify_multirun && $which_runtype > 1 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=2G\\n" . "threads_per_process=1\\n" baliphy_expanse_b perl $specify_mr perl " trees-consensus" 0 number_nodes1b 2 scheduler.conf perl !$more_memory && $specify_multiruns == 2 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=4G\\n" . "threads_per_process=2\\n" number_nodes1c 2 scheduler.conf perl !$more_memory && $specify_multiruns == 3 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=6G\\n" . "threads_per_process=3\\n" number_nodes1d 2 scheduler.conf perl !$more_memory && $specify_multiruns == 4 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=8G\\n" . "threads_per_process=4\\n" number_nodes1e 2 scheduler.conf perl !$more_memory && $specify_multiruns == 5 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=10G\\n" . "threads_per_process=5\\n" number_nodes1f 2 scheduler.conf perl !$more_memory && $specify_multiruns == 6 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=12G\\n" . "threads_per_process=6\\n" number_nodes2b 2 scheduler.conf perl $more_memory && !$specify_multirun && $which_runtype == 1 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=16G\\n" . "threads_per_process=2\\n" number_nodes2 2 scheduler.conf perl $more_memory && !$specify_multirun && $which_runtype > 1 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=8G\\n" . "threads_per_process=1\\n" number_nodes2b 2 scheduler.conf perl $more_memory && $specify_multiruns == 2 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=16G\\n" . "threads_per_process=2\\n" number_nodes2c 2 scheduler.conf perl $more_memory && $specify_multiruns == 3 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=24G\\n" . "threads_per_process=3\\n" number_nodes2d 2 scheduler.conf perl $more_memory && $specify_multiruns == 4 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=32G\\n" . "threads_per_process=4\\n" number_nodes2e 2 scheduler.conf perl $more_memory && $specify_multiruns == 5 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=40G\\n" . "threads_per_process=5\\n" number_nodes2f 2 scheduler.conf perl $more_memory && $specify_multiruns == 6 perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=48G\\n" . "threads_per_process=6\\n" input_file Input File sequences.fasta all_results * runtime 1 scheduler.conf Maximum Hours to Run (up to 168 hours) perl "runhours=$value\\n" 0.5 The maximum hours to run must be less than 168 perl $runtime > 168.0 The maximum hours to run must be greater than 0.05 perl $runtime < 0.05 Values in the config file will be overwritten by values configured in the interface perl defined $config_file BAli-Phy is quite CPU intensive, we recommend using 150 or fewer taxa in order to limit the time required to accumulate enough MCMC samples. perl $specify_tax > 150 The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 X $runtime cpu hours perl !$more_memory && !$specify_multirun && $which_runtype > 1 The job will run on 4 processors as configured. If it runs for the entire configured time, it will consume 4 X $runtime cpu hours perl !$more_memory && !$specify_multirun && $which_runtype == 1 The job will run on 2 processors as configured. If it runs for the entire configured time, it will consume 2 X $runtime cpu hours perl !$more_memory && $specify_multiruns == 2 The job will run on 3 processors as configured. If it runs for the entire configured time, it will consume 3 X $runtime cpu hours perl !$more_memory && $specify_multiruns == 3 The job will run on 4 processors as configured. If it runs for the entire configured time, it will consume 4 X $runtime cpu hours perl !$more_memory && $specify_multiruns == 4 The job will run on 5 processors as configured. If it runs for the entire configured time, it will consume 5 X $runtime cpu hours perl !$more_memory && $specify_multiruns == 5 The job will run on 6 processors as configured. If it runs for the entire configured time, it will consume 6 X $runtime cpu hours perl !$more_memory && $specify_multiruns == 6 The job will run on 4 processors as configured. If it runs for the entire configured time, it will consume 4 X $runtime cpu hours perl $more_memory && !$specify_multirun && $which_runtype > 1 The job will run on 8 processors as configured. If it runs for the entire configured time, it will consume 8 X $runtime cpu hours perl $more_memory && !$specify_multirun && $which_runtype == 1 The job will run on 8 processors as configured. If it runs for the entire configured time, it will consume 8 X $runtime cpu hours perl $more_memory && $specify_multiruns == 2 The job will run on 12 processors as configured. If it runs for the entire configured time, it will consume 12 X $runtime cpu hours perl $more_memory && $specify_multiruns == 3 The job will run on 16 processors as configured. If it runs for the entire configured time, it will consume 16 X $runtime cpu hours perl $more_memory && $specify_multiruns == 4 The job will run on 20 processors as configured. If it runs for the entire configured time, it will consume 20 X $runtime cpu hours perl $more_memory && $specify_multiruns == 5 The job will run on 24 processors as configured. If it runs for the entire configured time, it will consume 24 X $runtime cpu hours perl $more_memory && $specify_multiruns == 6 BAli-Phy does NOT detect how many iterations is sufficient: You need to monitor convergence and kill it when done. Use the kill feature in the interface to kill it. Then you can use the restart feature to run calculate a consensus tree. perl $runtime > 0 At present, a BAli-Phy job cannot be restarted from a checkpoint. Instead, you can use restart without changing the parameter set to create a new run or set of runs in the same directory. It is also possible to change the command line and run a subsequent analysis, for example, calculating a consensus tree. perl $runtime > 0 Estimate the maximum time your job will need to run. We recommend testing initially with a < 0.5hr test run because Jobs set for 0.5 h or less dependably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may run sooner than jobs configured for the full 168 hours. which_runtype Which runtype do you wish to use? 1 Two chains, with bootstrap and consensus, run completes (no restart possible; default) 2 A single chain, complete the run with just selected commands (no restart possible) 3 I want to specify every step (restart allowed) 1 more_memory I need more memory specify_multirun I want to make multiple runs perl !$specify_mr && $which_runtype ne 1 This option will repeat any command line you create as many times as you specify specify_multiruns How many runs? perl $specify_multirun 2 2 3 3 4 4 5 5 6 6 This value specified how many command lines to run config_file Specify an Option file perl !$specify_mr perl (defined $value) ? "-c option_file.txt":"" 8 option_file.txt The option file contains a script with all the instructions for the run. If you specofy an option file, most other options will be disabled in the interface. Otherwise, many instructions in the options file might be overwritten. You may safely use any options that remain active when an options file is specified. random_seed Random seed (-s) perl !$specify_mr && !defined $config_file perl defined $value ? "-s $value":"" 8 Specify a seed to make individual runs identical. random_seedb perl defined $random_seed && $specify_multiruns > 1 && !$specify_mr perl "-s $random_seed" 26 random_seedc perl defined $random_seed && $specify_multiruns > 2 && !$specify_mr perl "-s $random_seed" 46 random_seedd perl defined $random_seed && $specify_multiruns > 3 && !$specify_mr perl "-s $random_seed" 66 random_seede perl defined $random_seed && $specify_multiruns > 4 && !$specify_mr perl "-s $random_seed" 80 random_seedf perl defined $random_seed && $specify_multiruns > 5 && !$specify_mr perl "-s $random_seed" 88 specify_dirname Name for the analysis directory perl !defined $config_file Please enter a name for the analysis directory perl !defined $specify_dirname 10 num_iterations2 Number of iterations to run (-i; default run type) perl !$specify_mr && !defined $config_file && $which_runtype == 1 1000 12 Please enter the number of desired iterations perl !defined $num_iterations2 num_iterations Number of iterations to run (-i; other run types) perl !$specify_mr && !defined $config_file && $which_runtype > 1 200000 12 Please enter the number of desired iterations perl !defined $num_iterations && !defined $num_iterations2 specify_partitioned This is a partitioned analysis perl !$specify_mr && !defined $config_file specify_multiparts How many partitions? perl $specify_partitioned && !defined $config_file 2 2 3 3 4 4 5 5 6 6 specify_wrapup Wrap everything up at the end, this is my last run perl !$specify_mr && !defined $config_file 1 This option will zip up all your directories at the end of the run. If you want to restart a BAli-Phy run to add to the number of runs, or to continue the analysis, do not choose this option. However, if you are ready to download all your results at the end of this run, use this option. config_fileb perl defined $config_file && $specify_multiruns > 1 && !$specify_mr perl "-c option_file.txt" 26 config_filec perl defined $config_file && $specify_multiruns > 2 && !$specify_mr perl "-c option_file.txt" 46 config_filed Specify an Option file perl defined $config_file && $specify_multiruns > 3 && !$specify_mr perl "-c option_file.txt" 66 config_filee perl defined $config_file && $specify_multiruns > 4 && !$specify_mr perl "-c option_file.txt" 80 config_filef perl defined $config_file && $specify_multiruns > 5 && !$specify_mr perl "-c option_file.txt" 88 tree_file Specify a starting tree perl !$specify_mr && !defined $config_file perl (defined $value) ? "--tree tree.tre":"" 8 tree.tre tree_fileb perl defined $tree_file && $specify_multiruns > 1 && !$specify_mr perl "--tree tree.tre" 26 tree_filec perl defined $tree_file && $specify_multiruns > 2 && !$specify_mr perl "--tree tree.tre" 46 tree_filed perl defined $tree_file && $specify_multiruns > 3 && !$specify_mr perl "--tree tree.tre" 66 tree_filee perl defined $tree_file && $specify_multiruns > 4 && !$specify_mr perl "--tree tree.tre" 80 tree_filef perl defined $tree_file && $specify_multiruns > 5 && !$specify_mr perl "--tree tree.tre" 88 test_only Analyze the initial values and exit (-test) perl !$specify_multirun &&!$specify_mr && !defined $config_file perl ($value) ? "--test":"" 8 Configure_Gene1 Configure Partition 1 analysis datatype Choose the data type for Partition 1 (--alphabet) perl !$specify_mr && !defined $config_file 14 DNA DNA RNA RNA Amino-Acids Amino-Acids Codons Codons Triplets Triplets Please select a data type perl !defined $datatype substitution_model Choose the Substitution Model for Partition 1 (-S) perl !$specify_mr && !defined $config_file f81 F81 (all) jc69 JC69 (all) gtr GTR (all) k80 K80 (DNA/RNA) hky85 HKY85 (DNA/RNA) tn93 TN93 (DNA/RNA) jtt JTT (Amino-Acid) wag WAG (Amino-Acid) lg08 LG (Amino-Acid) HKY+x3 HKYx3 (Triplet) TN93+x3 TNx3 (Triplet) GTR+x3 GTRx3 (Triplet) gy94 GY94 (Codon) mg94 MG94 (Codon) gtr_sym+gy94 GY94[GTR] (Codon) Sorry, the HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model eq "hky85" || $substitution_model eq "tn93" ) && (defined $datatype && $datatype ne "RNA" && $datatype ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model eq "lg08" || $substitution_model eq "jtt" || $substitution_model eq "wag") && (defined $datatype && $datatype ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model eq "HKY+x3" || $substitution_model eq " TN93+x3" || $substitution_model eq "GTR+x3") && (defined $datatype && $datatype ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model eq "gy94" || $substitution_model eq "gtr_sym+gy94") && (defined $datatype && $datatype ne "Codons") gammarates41 perl defined $substitution_model Use Gamma[4] for Partition 1 +Rates.gamma[4] yes no invariable1 Allow invariant sites for Partition 1 perl defined $substitution_model +inv yes no model_type_1 Specify the insertion-deletion model for Partition 1 (-I) perl !$specify_mr && !defined $config_file rs07 RS07 rs05 RS05 none no Configure_Gene2 Configure Partition 2 analysis input_file2 Specify a second partition file perl $specify_partitioned && !defined $config_file sequences2.fasta Please select a second partition file perl !defined $input_file2 && $specify_multiparts > 1 In addition to using the command line, you may also specify options in a file. Option files also use the long form of command line options. Each option is given on its own line using the syntax "option = value" instead of the syntax "--option value". The value can be blank if the option does not take an argument. The align option indicates sequence files. Lines that begin with # are comments, and blank lines are ignored. datatype_2 Choose the data type for Partition 2 (--alphabet) 20 perl defined $input_file2 DNA DNA RNA RNA Amino-Acids Amino-Acids Codons Codons Triplets Triplets substitution_model2 Choose the Substitution Model for Partition 2 (-S) perl defined $input_file2 f81 F81 (all) jc69 JC69 (all) gtr GTR (all) k80 K80 (DNA/RNA) hky85 HKY85 (DNA/RNA) tn93 TN93 (DNA/RNA) jtt JTT (Amino-Acid) wag WAG (Amino-Acid) lg08 LG (Amino-Acid) HKY+x3 HKYx3 (Triplet) TN93+x3 TNx3 (Triplet) GTR+x3 GTRx3 (Triplet) gy94 GY94 (Codon) mg94 MG94 (Codon) gtr_sym+gy94 GY94[GTR] (Codon) Sorry, the HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model2 eq "hky85" || $substitution_model2 eq "tn93" ) && ($datatype_2 ne "RNA" && $datatype_2 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model2 eq "lg08" || $substitution_model2 eq "jtt" || $substitution_model2 eq "wag") && (defined $datatype_2 && $datatype_2 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model2 eq "HKY+x3" || $substitution_model2 eq " TN93+x3" || $substitution_model2 eq "GTR+x3") && (defined $datatype_2 && $datatype_2 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model2 eq "gy94" || $substitution_model2 eq "gtr_sym+gy94") && (defined $datatype_2 && $datatype_2 ne "Codons") gammarates42 Use Gamma[4] for Partition 2 perl defined $substitution_model2 +Rates.gamma[4] yes no Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && ((defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && ((defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && ((defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && ((defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && ((defined $invariable1 && !defined $invariable6) || (defined $invariable5 && !defined $invariable6)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && ((defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && ((defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && ((defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && ((defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && ((defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && ((defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && ((defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && ((defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5)) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $gammarates42) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile23 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && ((defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && ((defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && ((defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && ((defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && ((defined $gammarates41 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates46)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && ((defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && ((defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && ((defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && ((defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && ((defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && ((defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && ((defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && ((defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && ((defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && ((defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && ((defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && ((defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && ((defined $invariable1 && !defined $invariable6) || (defined $invariable5 && !defined $invariable6)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && ((defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && ((defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && ((defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && ((defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && ((defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && ((defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && ((defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && ((defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5)) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable2) || (defined $invariable2 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable3) || (defined $invariable3 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable3) || (defined $invariable3 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $invariable1 && !defined $invariable4) || (defined $invariable4 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $invariable2 && !defined $invariable4) || (defined $invariable4 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $invariable3 && !defined $invariable4) || (defined $invariable4 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable1 && !defined $invariable5) || (defined $invariable5 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable1 && !defined $invariable6) || (defined $invariable6 && !defined $invariable1) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable2 && !defined $invariable5) || (defined $invariable5 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable3 && !defined $invariable5) || (defined $invariable5 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $invariable4 && !defined $invariable5) || (defined $invariable5 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable2 && !defined $invariable6) || (defined $invariable6 && !defined $invariable2) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable3 && !defined $invariable6) || (defined $invariable6 && !defined $invariable3) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable4 && !defined $invariable6) || (defined $invariable6 && !defined $invariable4) ) Please make sure Invariable is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $invariable5 && !defined $invariable6) || (defined $invariable6 && !defined $invariable5) ) invariable2 Allow invariant sites for Partition 2 perl defined $substitution_model2 +inv yes no model_type_2 Specify the insertion-deletion model for Partition 2 (-I) perl defined $input_file2 rs07 RS07 rs05 RS05 none no Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $model_type_1 && defined $model_type_2 && ($model_type_1 ne $model_type_2) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $model_type_1 && defined $model_type_3 && ($model_type_1 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $model_type_1 && defined $model_type_4 && ($model_type_1 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $model_type_1 && defined $model_type_5 && ($model_type_1 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $model_type_1 && defined $model_type_6 && ($model_type_1 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $model_type_2 && defined $model_type_3 && ($model_type_2 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $model_type_2 && defined $model_type_4 && ($model_type_2 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $model_type_2 && defined $model_type_5 && ($model_type_2 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $model_type_2 && defined $model_type_6 && ($model_type_2 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $model_type_3 && defined $model_type_4 && ($model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $model_type_3 && defined $model_type_5 && ($model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $model_type_3 && defined $model_type_6 && ($model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $model_type_4 && defined $model_type_5 && ($model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $model_type_4 && defined $model_type_6 && ($model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $model_type_5 && defined $model_type_6 && ($model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_3 || $model_type_2 != $model_type_3 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_4 || $model_type_2 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_5 || $model_type_2 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_6 || $model_type_2 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_1 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 != $model_type_5 || $model_type_1 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 != $model_type_5 || $model_type_2 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 != $model_type_5 || $model_type_3 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_4 != $model_type_5 || $model_type_4 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 ne $model_type_4 || $model_type_2 ne $model_type_4 || $model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $model_type_1 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the -I value the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $model_type_1 && defined $model_type_2 && ($model_type_1 ne $model_type_2) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $model_type_1 && defined $model_type_3 && ($model_type_1 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $model_type_1 && defined $model_type_4 && ($model_type_1 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $model_type_1 && defined $model_type_5 && ($model_type_1 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $model_type_1 && defined $model_type_6 && ($model_type_1 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $model_type_2 && defined $model_type_3 && ($model_type_2 ne $model_type_3) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $model_type_2 && defined $model_type_4 && ($model_type_2 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $model_type_2 && defined $model_type_5 && ($model_type_2 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $model_type_2 && defined $model_type_6 && ($model_type_2 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $model_type_3 && defined $model_type_4 && ($model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $model_type_3 && defined $model_type_5 && ($model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $model_type_3 && defined $model_type_6 && ($model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $model_type_4 && defined $model_type_5 && ($model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $model_type_4 && defined $model_type_6 && ($model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $model_type_5 && defined $model_type_6 && ($model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_3 || $model_type_2 != $model_type_3 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_4 || $model_type_2 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_5 || $model_type_2 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && ($model_type_1 != $model_type_2 || $model_type_1 != $model_type_6 || $model_type_2 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 != $model_type_3 || $model_type_1 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 != $model_type_4 || $model_type_1 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_1 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 != $model_type_5 || $model_type_1 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_4 || $model_type_3 != $model_type_4 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_5 || $model_type_3 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_2 != $model_type_3 || $model_type_2 != $model_type_6 || $model_type_3 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 != $model_type_4 || $model_type_2 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 != $model_type_5 || $model_type_2 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_5 || $model_type_4 != $model_type_5 ) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_3 != $model_type_4 || $model_type_3 != $model_type_6 || $model_type_4 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 != $model_type_5 || $model_type_3 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_4 != $model_type_5 || $model_type_4 != $model_type_6 || $model_type_5 != $model_type_6 ) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && ($model_type_1 ne $model_type_4 || $model_type_2 ne $model_type_4 || $model_type_3 ne $model_type_4) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_3 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_2 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_2 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_2 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_1 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_1 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_1 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && ($model_type_2 ne $model_type_5 || $model_type_3 ne $model_type_5 || $model_type_4 ne $model_type_5) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_4 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_2 && defined $model_type_3 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_3 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_2 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_2 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Please make the -I value the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $model_type_3 && defined $model_type_4 && defined $model_type_5 && defined $model_type_6 && ($model_type_3 ne $model_type_6 || $model_type_4 ne $model_type_6 || $model_type_5 ne $model_type_6) Configure_Partition3 Configure Partition 3 analysis input_file3 Specify a third input file sequences3.fasta perl $specify_partitioned && defined $input_file2 && !defined $config_file Please select a third partition file perl !defined $input_file3 && $specify_multiparts > 2 datatype_3 Choose the data type for Partition 3 (--alphabet) perl defined $input_file3 DNA DNA RNA RNA Amino-Acids Amino-Acids Codons Codons Triplets Triplets substitution_model3 Choose the Substitution Model for Partition 3 (-S) perl defined $input_file3 f81 F81 (all) jc69 JC69 (all) gtr GTR (all) k80 K80 (DNA/RNA) hky85 HKY85 (DNA/RNA) tn93 TN93 (DNA/RNA) jtt JTT (Amino-Acid) wag WAG (Amino-Acid) lg08 LG (Amino-Acid) HKY+x3 HKYx3 (Triplet) TN93+x3 TNx3 (Triplet) GTR+x3 GTRx3 (Triplet) gy94 GY94 (Codon) mg94 MG94 (Codon) gtr_sym+gy94 GY94[GTR] (Codon) Sorry, the HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model3 eq "hky85" || $substitution_model3 eq "tn93" ) && (defined $datatype_3 && $datatype_3 ne "RNA" && $datatype_3 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model3 eq "lg08" || $substitution_model3 eq "jtt" || $substitution_model3 eq "wag") && (defined $datatype_3 && $datatype_3 ne "Amino-Acids") Sorry, the HKY+x3, TN93+x3, and GTR+x3 models can only be used for Triplet data perl ($substitution_model3 eq "HKY+x3" || $substitution_model3 eq "TN93+x3" || $substitution_model3 eq "GTR+x3") && (defined $datatype_3 && $datatype_3 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model3 eq "gy94" || $substitution_model3 eq "gtr_sym+gy94") && (defined $datatype_3 && $datatype_3 ne "Codons") gammarates43 Use Gamma[4] for Partition 3 perl defined $substitution_model3 +Rates.gamma[4] yes no invariable3 Allow invariant sites for Partition 3 perl defined $substitution_model3 +inv yes no model_type_3 Specify the insertion-deletion model for Partition 3 (-I) perl defined $input_file3 rs07 RS07 rs05 RS05 none no Configure_Partition4 Configure Partition 4 analysis input_file4 Specify a fourth input file sequences4.fasta perl defined $input_file3 && $specify_partitioned && !defined $config_file Please select a fourth partition file perl !defined $input_file4 && $specify_multiparts > 3 datatype_4 Choose the data type for Partition 4 (--alphabet) 22 perl defined $input_file4 DNA DNA RNA RNA Amino-Acids Amino-Acids Codons Codons Triplets Triplets substitution_model4 Choose the Substitution Model for Partition 4 (-S) perl defined $input_file4 22 f81 F81 (all) jc69 JC69 (all) gtr GTR (all) k80 K80 (DNA/RNA) hky85 HKY85 (DNA/RNA) tn93 TN93 (DNA/RNA) jtt JTT (Amino-Acid) wag WAG (Amino-Acid) lg08 LG (Amino-Acid) HKY+x3 HKYx3 (Triplet) TN93+x3 TNx3 (Triplet) GTR+x3 GTRx3 (Triplet) gy94 GY94 (Codon) mg94 MG94 (Codon) gtr_sym+gy94 GY94[GTR] (Codon) Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model4 eq "hky85" || $substitution_model4 eq "tn93" ) && (defined $datatype_4 && $datatype_4 ne "RNA" && $datatype_4 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model4 eq "lg08" || $substitution_model4 eq "jtt" || $substitution_model4 eq "wag") && (defined $datatype_4 && $datatype_4 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model4 eq "HKY+x3" || $substitution_model4 eq " TN93+x3" || $substitution_model4 eq "GTR+x3") && (defined $datatype_4 && $datatype_4 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model4 eq "gy94" || $substitution_model4 eq "gtr_sym+gy94") && (defined $datatype_4 && $datatype_4 ne "Codons") gammarates44 Use Gamma[4] for Partition 4 perl defined $substitution_model4 +Rates.gamma[4] yes no invariable4 Allow invariant sites for Partition 4 perl defined $substitution_model4 +inv yes no model_type_4 Specify the insertion-deletion model for Partition 4 (-I) perl defined $input_file4 rs07 RS07 rs05 RS05 none no 22 Configure_Partition5 Configure Partition 5 analysis input_file5 Specify a fifth input file sequences5.fasta perl $specify_partitioned && defined $input_file4 && !defined $config_file Please select a fifth partition file perl !defined $input_file5 && $specify_multiparts > 4 datatype_5 Choose the data type for Partition 5 (--alphabet) 22 perl defined $input_file5 DNA DNA RNA RNA Amino-Acids Amino-Acids Codons Codons Triplets Triplets substitution_model5 Choose the Substitution Model for Partition 5 (-S) perl defined $input_file5 f81 F81 (all) jc69 JC69 (all) gtr GTR (all) k80 K80 (DNA/RNA) hky85 HKY85 (DNA/RNA) tn93 TN93 (DNA/RNA) jtt JTT (Amino-Acid) wag WAG (Amino-Acid) lg08 LG (Amino-Acid) HKY+x3 HKYx3 (Triplet) TN93+x3 TNx3 (Triplet) GTR+x3 GTRx3 (Triplet) gy94 GY94 (Codon) mg94 MG94 (Codon) gtr_sym+gy94 GY94[GTR] (Codon) Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model5 eq "hky85" || $substitution_model5 eq "tn93" ) && (defined $datatype_5 && $datatype_5 ne "RNA" && $datatype_5 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model5 eq "lg08" || $substitution_model5 eq "jtt" || $substitution_model5 eq "wag") && (defined $datatype_5 && $datatype_5 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model5 eq "HKY+x3" || $substitution_model5 eq " TN93+x3" || $substitution_model5 eq "GTR+x3") && (defined $datatype_5 && $datatype_5 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model5 eq "gy94" || $substitution_model5 eq "gtr_sym+gy94") && (defined $datatype_5 && $datatype_5 ne "Codons") gammarates45 Use Gamma[4] for Partition 5 perl defined $substitution_model5 +Rates.gamma[4] yes no invariable5 Allow invariant sites for Partition 5 perl defined $substitution_model5 +inv yes no model_type_5 Specify the insertion-deletion model for Partition 5 (-I) perl defined $input_file5 rs07 RS07 rs05 RS05 none no 22 Configure_Partition6 Configure Partition 6 analysis input_file6 Specify a sixth input file sequences6.fasta perl $specify_partitioned && defined $input_file5 && !defined $config_file Please select a sixth partition file perl !defined $input_file6 && $specify_multiparts > 5 datatype_6 Choose the data type for Partition 6 (--alphabet) 22 perl defined $input_file6 DNA DNA RNA RNA Amino-Acids Amino-Acids Codons Codons Triplets Triplets substitution_model6 Choose the Substitution Model for Partition 6 (-S) perl defined $input_file6 22 f81 F81 (all) jc69 JC69 (all) gtr GTR (all) k80 K80 (DNA/RNA) hky85 HKY85 (DNA/RNA) tn93 TN93 (DNA/RNA) jtt JTT (Amino-Acid) wag WAG (Amino-Acid) lg08 LG (Amino-Acid) HKY+x3 HKYx3 (Triplet) TN93+x3 TNx3 (Triplet) GTR+x3 GTRx3 (Triplet) gy94 GY94 (Codon) mg94 MG94 (Codon) gtr_sym+gy94 GY94[GTR] (Codon) Sorry, the GTR, HKY85, and TN93 models can only be used for DNA or RNA data perl ($substitution_model6 eq "hky85" || $substitution_model6 eq "tn93" ) && (defined $datatype_6 && $datatype_6 ne "RNA" && $datatype_6 ne "DNA") Sorry, the LG, JTT, and WAG models can only be used for Amino Acid data perl ($substitution_model6 eq "lg08" || $substitution_model6 eq "jtt" || $substitution_model6 eq "wag") && (defined $datatype_6 && $datatype_6 ne "Amino-Acids") Sorry, the HKYx3, TNx3, and GTRx3 models can only be used for Triplet data perl ($substitution_model6 eq "HKY+x3" || $substitution_model6 eq " TN93+x3" || $substitution_model6 eq "GTR+x3") && (defined $datatype_6 && $datatype_6 ne "Triplets") Sorry, the GY94 and GY94[GTR] models can only be used for Codon data perl ($substitution_model6 eq "gy94" || $substitution_model6 eq "gtr_sym+gy94") && (defined $datatype_6 && $datatype_6 ne "Codons") gammarates46 Use Gamma[4] for Partition 6 perl defined $substitution_model6 +Rates.gamma[4] yes no invariable6 Allow invariant sites for Partition 6 perl defined $substitution_model6 +inv yes no model_type_6 Specify the insertion-deletion model for Partition 6 (-I) perl defined $input_file6 rs07 RS07 rs05 RS05 none no 22 mcmc_options Model Options subsample_factor Factor by which to subsample (-x) perl !$specify_mr && !defined $config_file perl ($value != $vdef) ? "-x $value":"" 1 22 The optimal value for subsample factor is one in most cases perl $subsample_factor != "1" The number supplied here determines how often to sample. For example -x 10 keep every 10th sample. 1 is the best value link_specified_h perl defined $linkfile1 && defined $linkfile2 && !defined $linkfile3 perl "--link $linkfile1,$linkfile2" 18 link_specified_hb perl $specify_multiruns > 1 && defined $linkfile1 && defined $linkfile2 && !defined $linkfile3 perl "--link $linkfile1,$linkfile2" 33 link_specified_hc perl $specify_multiruns > 2 && defined $linkfile1 && defined $linkfile2 && !defined $linkfile3 perl "--link $linkfile1,$linkfile2" 53 link_specified_hd perl $specify_multiruns > 3 && defined $linkfile1 && defined $linkfile2 && !defined $linkfile3 perl "--link $linkfile1,$linkfile2" 71 link_specified_he perl $specify_multiruns > 4 && defined $linkfile1 && defined $linkfile2 && !defined $linkfile3 perl "--link $linkfile1,$linkfile2" 82 link_specified_hf perl $specify_multiruns > 5 && defined $linkfile1 && defined $linkfile2 && !defined $linkfile3 perl "--link $linkfile1,$linkfile2" 90 link_specified_h2 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && !defined $linkfile4 perl "--link $linkfile1,$linkfile2,$linkfile3" 18 link_specified_h2b perl $specify_multiruns > 1 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && !defined $linkfile4 perl "--link $linkfile1,$linkfile2,$linkfile3" 33 link_specified_h2c perl $specify_multiruns > 2 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && !defined $linkfile4 perl "--link $linkfile1,$linkfile2,$linkfile3" 53 link_specified_h2d perl $specify_multiruns > 3 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && !defined $linkfile4 perl "--link $linkfile1,$linkfile2,$linkfile3" 71 link_specified_h2e perl $specify_multiruns > 4 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && !defined $linkfile4 perl "--link $linkfile1,$linkfile2,$linkfile3" 82 link_specified_h2f perl $specify_multiruns > 5 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && !defined $linkfile4 perl "--link $linkfile1,$linkfile2,$linkfile3" 90 link_specified_h3 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && !defined $linkfile5 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4" 18 link_specified_h3b perl $specify_multiruns > 1 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && !defined $linkfile5 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4" 33 link_specified_h3c perl $specify_multiruns > 2 &&defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && !defined $linkfile5 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4" 53 link_specified_h3d perl $specify_multiruns > 3 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && !defined $linkfile5 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4" 71 link_specified_h3e perl $specify_multiruns > 4 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && !defined $linkfile5 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4" 82 link_specified_h3f perl $specify_multiruns > 5 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && !defined $linkfile5 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4" 90 link_specified_h4 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && !defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,linkfile5" 18 link_specified_h4b perl $specify_multiruns > 1 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && !defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,linkfile5" 33 link_specified_h4c perl $specify_multiruns > 2 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && !defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,linkfile5" 53 link_specified_h4d perl $specify_multiruns > 3 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && !defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,linkfile5" 72 link_specified_h4e perl $specify_multiruns > 4 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && !defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,linkfile5" 82 link_specified_h4f perl $specify_multiruns > 5 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && !defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,linkfile5" 90 link_specified_h5 perl defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,$linkfile5,$linkfile6" 18 link_specified_h5b perl $specify_multiruns > 1 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,$linkfile5,$linkfile6" 33 link_specified_h5c perl $specify_multiruns > 2 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,$linkfile5,$linkfile6" 53 link_specified_h5d perl $specify_multiruns > 3 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,$linkfile5,$linkfile6" 72 link_specified_h5e perl $specify_multiruns > 4 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,$linkfile5,$linkfile6" 81 link_specified_h5f perl $specify_multiruns > 5 && defined $linkfile1 && defined $linkfile2 && defined $linkfile3 && defined $linkfile4 && defined $linkfile5 && defined $linkfile6 perl "--link $linkfile1,$linkfile2,$linkfile3,$linkfile4,$linkfile5,$linkfile6" 90 link_specified_h21 perl defined $linkfile21 && defined $linkfile22 && !defined $linkfile23 perl "--link $linkfile21,$linkfile22" 18 link_specified_h21b perl $specify_multiruns > 1 && defined $linkfile21 && defined $linkfile22 && !defined $linkfile23 perl "--link $linkfile21,$linkfile22" 33 link_specified_h21c perl $specify_multiruns > 2 && defined $linkfile21 && defined $linkfile22 && !defined $linkfile23 perl "--link $linkfile21,$linkfile22" 53 link_specified_h21d perl $specify_multiruns > 3 && defined $linkfile21 && defined $linkfile22 && !defined $linkfile23 perl "--link $linkfile21,$linkfile22" 72 link_specified_h21e perl $specify_multiruns > 4 && defined $linkfile21 && defined $linkfile22 && !defined $linkfile23 perl "--link $linkfile21,$linkfile22" 82 link_specified_h21f perl $specify_multiruns > 5 && defined $linkfile21 && defined $linkfile22 && !defined $linkfile23 perl "--link $linkfile21,$linkfile22" 90 link_specified_h22 perl defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && !defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23" 18 link_specified_h22b perl $specify_multiruns > 1 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && !defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23" 33 link_specified_h22c perl $specify_multiruns > 2 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && !defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23" 53 link_specified_h22d perl $specify_multiruns > 3 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && !defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23" 71 link_specified_h22e perl $specify_multiruns > 4 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && !defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23" 82 link_specified_h22f perl $specify_multiruns > 5 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && !defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23" 90 link_specified_h23 perl defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23,$linkfile24" 18 link_specified_h23b perl $specify_multiruns > 1 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23,$linkfile24" 33 link_specified_h23c perl $specify_multiruns > 2 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23,$linkfile24" 53 link_specified_h23d perl $specify_multiruns > 3 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23,$linkfile24" 71 link_specified_h23e perl $specify_multiruns > 4 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23,$linkfile24" 82 link_specified_h23f perl $specify_multiruns > 5 && defined $linkfile21 && defined $linkfile22 && defined $linkfile23 && defined $linkfile24 perl "--link $linkfile21,$linkfile22,$linkfile23,$linkfile24" 90 link_models Linking model options Group of Genes to Link Select a group of Genes to Link linkfile1 Select the first gene to link (choose the lowest value first) perl $specify_partitioned && !$specify_mr 1 1 2 2 3 3 4 4 5 5 6 6 Please enter the lowest gene number first perl $linkfile1 > $linkfile2 Sorry, a given gene can only be linked once perl defined $linkfile1 && defined $linkfile2 && ($linkfile1 eq $linkfile21 || $linkfile1 eq $linkfile22 || $linkfile2 eq $linkfile21 || $linkfile2 eq $linkfile22 ) Sorry, a given gene can only be linked once perl defined $linkfile1 && defined $linkfile2 && ($linkfile1 eq $linkfile23 || $linkfile1 eq $linkfile24 || $linkfile2 eq $linkfile23 || $linkfile2 eq $linkfile24 ) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile1 && defined $linkfile2 && ($linkfile1 eq $linkfile2) Please select at least one more gene (up to six) to link perl defined $linkfile1 && !defined $linkfile2 Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $datatype && defined $datatype_2 && ($datatype ne $datatype_2) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $datatype && defined $datatype_3 && ($datatype ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $datatype && defined $datatype_4 && ($datatype ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $datatype && defined $datatype_5 && ($datatype ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $datatype && defined $datatype_6 && ($datatype ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $datatype_2 && defined $datatype_3 && ($datatype_2 ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $datatype_2 && defined $datatype_4 && ($datatype_2 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $datatype_2 && defined $datatype_5 && ($datatype_2 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $datatype_2 && defined $datatype_6 && ($datatype_2 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $datatype_3 && defined $datatype_4 && ($datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $datatype_3 && defined $datatype_5 && ($datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $datatype_3 && defined $datatype_6 && ($datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $datatype_4 && defined $datatype_5 && ($datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $datatype_4 && defined $datatype_6 && ($datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $datatype_5 && defined $datatype_6 && ($datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_3 || $datatype_2 != $datatype_3 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_4 && ($datatype != $datatype_2 || $datatype != $datatype_4 || $datatype_2 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_5 && ($datatype != $datatype_2 || $datatype != $datatype_5 || $datatype_2 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_6 || $datatype_2 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $datatype && defined $datatype_3 && defined $datatype_4 && ($datatype != $datatype_3 || $datatype != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_5 && ($datatype != $datatype_3 || $datatype != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_6 && ($datatype != $datatype_3 || $datatype != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $datatype && defined $datatype_4 && defined $datatype_5 && ($datatype != $datatype_4 || $datatype != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_6 && ($datatype != $datatype_4 || $datatype != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype && defined $datatype_5 && defined $datatype_6 && ($datatype != $datatype_5 || $datatype != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 != $datatype_5 || $datatype_2 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 != $datatype_5 || $datatype_3 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_4 != $datatype_5 || $datatype_4 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype ne $datatype_4 || $datatype_2 ne $datatype_4 || $datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $datatype && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the alphabet the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $substitution_model && defined $substitution_model2 && ($substitution_model ne $substitution_model2) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $substitution_model && defined $substitution_model3 && ($substitution_model ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $substitution_model && defined $substitution_model4 && ($substitution_model ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $substitution_model && defined $substitution_model5 && ($substitution_model ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $substitution_model && defined $substitution_model6 && ($substitution_model ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model2 ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model2 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $substitution_model2 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model3 || $substitution_model2 != $substitution_model3 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model4 || $substitution_model2 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model5 || $substitution_model2 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model6 || $substitution_model2 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model != $substitution_model5 || $substitution_model != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 != $substitution_model5 || $substitution_model2 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 != $substitution_model5 || $substitution_model3 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model4 != $substitution_model5 || $substitution_model4 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model ne $substitution_model4 || $substitution_model2 ne $substitution_model4 || $substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $substitution_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) linkfile2 Select the second gene to link (--link) perl !defined $config_file 1 1 2 2 3 3 4 4 5 5 6 6 Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && defined $custom_model && defined $custom_model2 && ($custom_model ne $custom_model2) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && defined $custom_model && defined $custom_model3 && ($custom_model ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && defined $custom_model && defined $custom_model4 && ($custom_model ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && defined $custom_model && defined $custom_model5 && ($custom_model ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && defined $custom_model && defined $custom_model6 && ($custom_model ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && defined $custom_model2 && defined $custom_model3 && ($custom_model2 ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && defined $custom_model2 && defined $custom_model4 && ($custom_model2 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && defined $custom_model2 && defined $custom_model5 && ($custom_model2 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && defined $custom_model2 && defined $custom_model6 && ($custom_model2 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && defined $custom_model3 && defined $custom_model4 && ($custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && defined $custom_model3 && defined $custom_model5 && ($custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && defined $custom_model3 && defined $custom_model6 && ($custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && defined $custom_model4 && defined $custom_model5 && ($custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && defined $custom_model4 && defined $custom_model6 && ($custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 5 && $linkfile2 == 6 && defined $custom_model5 && defined $custom_model6 && ($custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model3 || $custom_model2 != $custom_model3 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && ($custom_model != $custom_model2 || $custom_model != $custom_model4 || $custom_model2 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && ($custom_model != $custom_model2 || $custom_model != $custom_model5 || $custom_model2 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model6 || $custom_model2 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && ($custom_model != $custom_model3 || $custom_model != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && ($custom_model != $custom_model3 || $custom_model != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model6 && ($custom_model != $custom_model3 || $custom_model != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && ($custom_model != $custom_model4 || $custom_model != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model6 && ($custom_model != $custom_model4 || $custom_model != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model && defined $custom_model5 && defined $custom_model6 && ($custom_model != $custom_model5 || $custom_model != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 != $custom_model5 || $custom_model2 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 != $custom_model5 || $custom_model3 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model4 != $custom_model5 || $custom_model4 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model ne $custom_model4 || $custom_model2 ne $custom_model4 || $custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && ((defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && ((defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && ((defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && ((defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 6 && ((defined $gammarates41 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates46)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && ((defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && ((defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && ((defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 6 && ((defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && ((defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && ((defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 6 && ((defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 6 && ((defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && ((defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 4 && $linkfile2 == 5 && $linkfile3 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 3 && $linkfile2 == 4 && $linkfile3 == 5 && $linkfile4 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 2 && $linkfile2 == 3 && $linkfile3 == 4 && $linkfile4 == 5 && $linkfile5 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile1 == 1 && $linkfile2 == 2 && $linkfile3 == 3 && $linkfile4 == 4 && $linkfile5 == 5 && $linkfile6 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) linkfile3 Select the third gene to link (--link) perl defined $linkfile2 1 1 2 2 3 3 4 4 5 5 6 6 A given gene can only be linked once per run perl defined $linkfile3 && defined $linkfile21 && defined $linkfile22 && ($linkfile3 eq $linkfile21 || $linkfile3 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile3 && ($linkfile3 eq $linkfile1 || $linkfile3 eq $linkfile2) Please enter the lowest gene number first perl defined $linkfile3 && $linkfile2 > $linkfile3 linkfile4 Select the fourth gene to link (--link) perl defined $linkfile3 1 1 2 2 3 3 4 4 5 5 6 6 Sorry, a given gene can only be linked once per run perl defined $linkfile4 && defined $linkfile21 && defined $linkfile22 && ($linkfile4 eq $linkfile21 || $linkfile4 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile4 && ($linkfile4 eq $linkfile1 || $linkfile4 eq $linkfile2 || $linkfile4 eq $linkfile3) Please enter the lowest gene number first perl defined $linkfile4 && $linkfile3 > $linkfile4 linkfile5 Select the fifth gene to link (--link) perl defined $linkfile4 1 1 2 2 3 3 4 4 5 5 6 6 Sorry, a given gene can only be linked once per run perl defined $linkfile4 && defined $linkfile21 && defined $linkfile22 && ($linkfile4 eq $linkfile21 || $linkfile4 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile4 && ($linkfile4 eq $linkfile1 || $linkfile4 eq $linkfile2 || $linkfile4 eq $linkfile3) Please enter the lowest gene number first perl defined $linkfile4 && $linkfile3 > $linkfile4 linkfile6 Select the sixth gene to link (--link) perl defined $linkfile5 1 1 2 2 3 3 4 4 5 5 6 6 Sorry, a given gene can only be linked once per run perl defined $linkfile4 && defined $linkfile21 && defined $linkfile22 && ($linkfile4 eq $linkfile21 || $linkfile4 eq $linkfile22) Sorry, the same gene cannot be linked twice to the same group perl defined $linkfile4 && ($linkfile4 eq $linkfile1 || $linkfile4 eq $linkfile2 || $linkfile4 eq $linkfile3) Please enter the lowest gene number first perl defined $linkfile4 && $linkfile3 > $linkfile4 Second group of Genes to Link Select a second group of Genes to Link linkfile21 Select the first gene to link (--link) perl defined $linkfile1 && !defined $linkfile5 && !defined $config_file 1 1 2 2 3 3 4 4 5 5 6 6 linkfile22 Select the second gene to link (--link) perl defined $linkfile21 1 1 2 2 3 3 4 4 5 5 6 6 Sorry, the same gene cannot be selected twice for linking perl defined $linkfile21 && defined $linkfile22 && ($linkfile21 eq $linkfile22) Sorry, the same gene cannot be selected twice for linking perl defined $linkfile23 && ($linkfile21 eq $linkfile23 || $linkfile22 eq $linkfile23) Sorry, the same gene cannot be selected twice for linking perl defined $linkfile24 && ($linkfile21 eq $linkfile24 || $linkfile22 eq $linkfile24 || $linkfile22 eq $linkfile24) Please select one more gene to link perl defined $linkfile21 && !defined $linkfile22 Please enter the lowest gene number first perl defined $linkfile22 && $linkfile21 > $linkfile22 linkfile23 Select the third gene to link (--link) perl defined $linkfile22 1 1 2 2 3 3 4 4 5 5 6 6 Please enter the lowest gene number first perl defined $linkfile23 && $linkfile22 > $linkfile23 Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $datatype && defined $datatype_2 && ($datatype ne $datatype_2) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $datatype && defined $datatype_3 && ($datatype ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $datatype && defined $datatype_4 && ($datatype ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $datatype && defined $datatype_5 && ($datatype ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $datatype && defined $datatype_6 && ($datatype ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $datatype_2 && defined $datatype_3 && ($datatype_2 ne $datatype_3) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $datatype_2 && defined $datatype_4 && ($datatype_2 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $datatype_2 && defined $datatype_5 && ($datatype_2 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $datatype_2 && defined $datatype_6 && ($datatype_2 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $datatype_3 && defined $datatype_4 && ($datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $datatype_3 && defined $datatype_5 && ($datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $datatype_3 && defined $datatype_6 && ($datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $datatype_4 && defined $datatype_5 && ($datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $datatype_4 && defined $datatype_6 && ($datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $datatype_5 && defined $datatype_6 && ($datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_3 || $datatype_2 != $datatype_3 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_4 && ($datatype != $datatype_2 || $datatype != $datatype_4 || $datatype_2 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_5 && ($datatype != $datatype_2 || $datatype != $datatype_5 || $datatype_2 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && ($datatype != $datatype_2 || $datatype != $datatype_6 || $datatype_2 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $datatype && defined $datatype_3 && defined $datatype_4 && ($datatype != $datatype_3 || $datatype != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_5 && ($datatype != $datatype_3 || $datatype != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_6 && ($datatype != $datatype_3 || $datatype != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $datatype && defined $datatype_4 && defined $datatype_5 && ($datatype != $datatype_4 || $datatype != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_6 && ($datatype != $datatype_4 || $datatype != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype && defined $datatype_5 && defined $datatype_6 && ($datatype != $datatype_5 || $datatype != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_4 || $datatype_3 != $datatype_4 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_5 || $datatype_3 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype_2 != $datatype_3 || $datatype_2 != $datatype_6 || $datatype_3 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 != $datatype_4 || $datatype_2 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 != $datatype_5 || $datatype_2 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_5 || $datatype_4 != $datatype_5 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_3 != $datatype_4 || $datatype_3 != $datatype_6 || $datatype_4 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 != $datatype_5 || $datatype_3 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_4 != $datatype_5 || $datatype_4 != $datatype_6 || $datatype_5 != $datatype_6 ) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && ($datatype ne $datatype_4 || $datatype_2 ne $datatype_4 || $datatype_3 ne $datatype_4) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_3 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_2 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype && defined $datatype_2 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_2 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && ($datatype_2 ne $datatype_5 || $datatype_3 ne $datatype_5 || $datatype_4 ne $datatype_5) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_4 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_3 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_3 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_2 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_2 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the alphabet the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $datatype_3 && defined $datatype_4 && defined $datatype_5 && defined $datatype_6 && ($datatype_3 ne $datatype_6 || $datatype_4 ne $datatype_6 || $datatype_5 ne $datatype_6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $substitution_model && defined $substitution_model2 && ($substitution_model ne $substitution_model2) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $substitution_model && defined $substitution_model3 && ($substitution_model ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $substitution_model && defined $substitution_model4 && ($substitution_model ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $substitution_model && defined $substitution_model5 && ($substitution_model ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $substitution_model && defined $substitution_model6 && ($substitution_model ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model2 ne $substitution_model3) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model2 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $substitution_model2 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model3 || $substitution_model2 != $substitution_model3 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model4 || $substitution_model2 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model5 || $substitution_model2 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && ($substitution_model != $substitution_model2 || $substitution_model != $substitution_model6 || $substitution_model2 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model != $substitution_model3 || $substitution_model != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model != $substitution_model4 || $substitution_model != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model != $substitution_model5 || $substitution_model != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model4 || $substitution_model3 != $substitution_model4 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model5 || $substitution_model3 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model2 != $substitution_model3 || $substitution_model2 != $substitution_model6 || $substitution_model3 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 != $substitution_model4 || $substitution_model2 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 != $substitution_model5 || $substitution_model2 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model5 || $substitution_model4 != $substitution_model5 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model3 != $substitution_model4 || $substitution_model3 != $substitution_model6 || $substitution_model4 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 != $substitution_model5 || $substitution_model3 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model4 != $substitution_model5 || $substitution_model4 != $substitution_model6 || $substitution_model5 != $substitution_model6 ) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && ($substitution_model ne $substitution_model4 || $substitution_model2 ne $substitution_model4 || $substitution_model3 ne $substitution_model4) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model2 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model2 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model2 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && ($substitution_model2 ne $substitution_model5 || $substitution_model3 ne $substitution_model5 || $substitution_model4 ne $substitution_model5) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model2 && defined $substitution_model3 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model3 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model2 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model2 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) Please make the substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $substitution_model3 && defined $substitution_model4 && defined $substitution_model5 && defined $substitution_model6 && ($substitution_model3 ne $substitution_model6 || $substitution_model4 ne $substitution_model6 || $substitution_model5 ne $substitution_model6) linkfile24 Select the fourth gene to link (--link) perl defined $linkfile23 1 1 2 2 3 3 4 4 5 5 6 6 Please enter the lowest gene number first perl defined $linkfile24 && $linkfile23 > $linkfile24 Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && defined $custom_model && defined $custom_model2 && ($custom_model ne $custom_model2) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && defined $custom_model && defined $custom_model3 && ($custom_model ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && defined $custom_model && defined $custom_model4 && ($custom_model ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && defined $custom_model && defined $custom_model5 && ($custom_model ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && defined $custom_model && defined $custom_model6 && ($custom_model ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && defined $custom_model2 && defined $custom_model3 && ($custom_model2 ne $custom_model3) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && defined $custom_model2 && defined $custom_model4 && ($custom_model2 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && defined $custom_model2 && defined $custom_model5 && ($custom_model2 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && defined $custom_model2 && defined $custom_model6 && ($custom_model2 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && defined $custom_model3 && defined $custom_model4 && ($custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && defined $custom_model3 && defined $custom_model5 && ($custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && defined $custom_model3 && defined $custom_model6 && ($custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && defined $custom_model4 && defined $custom_model5 && ($custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && defined $custom_model4 && defined $custom_model6 && ($custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 5 && $linkfile22 == 6 && defined $custom_model5 && defined $custom_model6 && ($custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model3 || $custom_model2 != $custom_model3 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && ($custom_model != $custom_model2 || $custom_model != $custom_model4 || $custom_model2 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && ($custom_model != $custom_model2 || $custom_model != $custom_model5 || $custom_model2 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && ($custom_model != $custom_model2 || $custom_model != $custom_model6 || $custom_model2 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && ($custom_model != $custom_model3 || $custom_model != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && ($custom_model != $custom_model3 || $custom_model != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model6 && ($custom_model != $custom_model3 || $custom_model != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && ($custom_model != $custom_model4 || $custom_model != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model6 && ($custom_model != $custom_model4 || $custom_model != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model && defined $custom_model5 && defined $custom_model6 && ($custom_model != $custom_model5 || $custom_model != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model4 || $custom_model3 != $custom_model4 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model5 || $custom_model3 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model2 != $custom_model3 || $custom_model2 != $custom_model6 || $custom_model3 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 != $custom_model4 || $custom_model2 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 != $custom_model5 || $custom_model2 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model5 || $custom_model4 != $custom_model5 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model3 != $custom_model4 || $custom_model3 != $custom_model6 || $custom_model4 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 != $custom_model5 || $custom_model3 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model4 != $custom_model5 || $custom_model4 != $custom_model6 || $custom_model5 != $custom_model6 ) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && ($custom_model ne $custom_model4 || $custom_model2 ne $custom_model4 || $custom_model3 ne $custom_model4) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model3 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model2 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model && defined $custom_model2 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model2 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && ($custom_model2 ne $custom_model5 || $custom_model3 ne $custom_model5 || $custom_model4 ne $custom_model5) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model4 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model2 && defined $custom_model3 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model3 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model2 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model2 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make the custom substitution model the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && defined $custom_model3 && defined $custom_model4 && defined $custom_model5 && defined $custom_model6 && ($custom_model3 ne $custom_model6 || $custom_model4 ne $custom_model6 || $custom_model5 ne $custom_model6) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && ((defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && ((defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && ((defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && ((defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 6 && ((defined $gammarates41 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates46)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && ((defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && ((defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && ((defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 6 && ((defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && ((defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && ((defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 6 && ((defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 6 && ((defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && ((defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45)) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates42) || (defined $gammarates42 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates43) || (defined $gammarates43 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 4 && $linkfile22 == 5 && $linkfile23 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates41 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates42 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 4 && ( (defined $gammarates43 && !defined $gammarates44) || (defined $gammarates44 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 3 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 2 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates41 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates41 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates41) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 1 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates42 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates43 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 5 && ( (defined $gammarates44 && !defined $gammarates45) || (defined $gammarates45 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 4 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 3 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates42 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates42) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 2 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates43 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates43) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates44 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates44) ) Please make sure Use Gamma[4] is the same for all linked genes perl $linkfile21 == 3 && $linkfile22 == 4 && $linkfile23 == 5 && $linkfile24 == 6 && ( (defined $gammarates45 && !defined $gammarates46) || (defined $gammarates46 && !defined $gammarates45) ) Consensus_options Consensus Tree Options specify_mr Calculate majority rule trees perl !defined $config_file && $which_runtype > 1 specify_mrruns How many tree files? perl $specify_mr 2 2 3 3 4 4 5 5 6 6 specify_mr2 perl $specify_mr && $specify_mrruns == 2 perl "$specify_dirname-1/C1.trees $specify_dirname-2/C1.trees > c50.PP.tree" 40 specify_mr3 perl $specify_mr && $specify_mrruns == 3 perl "$specify_dirname-1/C1.trees $specify_dirname-2/C1.trees $specify_dirname-3/C1.trees > c50.PP.tree" 40 specify_mr4 perl $specify_mr && $specify_mrruns == 4 perl "$specify_dirname-1/C1.trees $specify_dirname-2/C1.trees $specify_dirname-3/C1.trees $specify_dirname-4/C1.trees > c50.PP.tree" 40 specify_mr5 perl $specify_mr && $specify_mrruns == 5 perl "$specify_dirname-1/C1.trees $specify_dirname-2/C1.trees $specify_dirname-3/C1.trees $specify_dirname-4/C1.trees $specify_dirname-5/C1.trees > c50.PP.tree" 40 specify_mr6 perl $specify_mr && $specify_mrruns == 6 perl "$specify_dirname-1/C1.trees $specify_dirname-2/C1.trees $specify_dirname-3/C1.trees $specify_dirname-4/C1.trees $specify_dirname-5/C1.trees $specify_dirname-6/C1.trees > c50.PP.tree" 40 specify_burnin Specify percent of trees to burnin (-s) perl $specify_mr perl ($value ne $vdef) ? "-s $value%":"" 31 10 Sorry, you cant specify both a percentage and an explicit number of burnin trees perl defined $specify_burnin && defined $specify_burnin2 specify_burnin2 Specify number of trees to burnin (-s) perl $specify_mr perl (defined $value) ? "-s $value":"" 32 specify_subsample perl $specify_mr Count every nth tree (-x) perl ($value ne $vdef) ? "-x $value":"" 33 1 specify_stringency Specify splits stringency (-*consensus-PP) perl $specify_mr perl ($value ne $vdef) ? "--consensus-PP $value":"" 0.5 34 specify_stringency2 Specify splits stringency (--consensus) perl $specify_mr perl (defined $value) ? "--consensus $value":"" 35