RAxML-HPC2 Workflow on XSEDE 8.2.12 Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE Alexandros Stamatakis Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.Bioinformatics. 2006 Nov 1;22(21):2688-90 Phylogeny / Alignment http://icwww.epfl.ch/~stamatak/index-Dateien/countManual7.0.0.php raxmlhpc2_workflow this_is_a_workflow scheduler.conf perl "workflow_type=simple\\n" 0 raxmlhpc_hybridlogic1 perl $datatype ne "protein" && $specify_workflow ne "FTS" && $nchar < 500000 && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) perl "raxmlHPC-HYBRID_8.2.12_expanse" 0 raxmlhpc_hybridlogic2 perl $datatype eq "protein" && $specify_workflow ne "FTS" && $nchar < 200000 && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) perl "raxmlHPC-HYBRID_8.2.12_expanse" 0 raxmlhpc_hybridlogic3 perl $datatype ne "protein" && $specify_workflow ne "FTS" && $nchar > 499999 && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) perl "raxmlHPC-PTHREADS_8.2.12_expanse" 0 raxmlhpc_hybridlogic4 perl $datatype eq "protein" && $specify_workflow ne "FTS" && $nchar > 199999 && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) perl "raxmlHPC-PTHREADS_8.2.12_expanse" 0 raxmlhpc_fasttreesearch1hyb_scheduler scheduler.conf perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar < 10000 perl "jobtype=mpi\\n" . "mpi_processes=10\\n" . "threads_per_process=4\\n" . "cpus-per-task=4\\n" . "mem=77G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch2hyb_scheduler scheduler.conf perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 9999 && $nchar < 40000 perl "jobtype=mpi\\n" . "mpi_processes=5\\n" . "threads_per_process=25\\n" . "cpus-per-task=25\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch3hyb_scheduler scheduler.conf perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 39999 && $nchar < 500000 perl "jobtype=mpi\\n" . "mpi_processes=2\\n" . "threads_per_process=64\\n" . "cpus-per-task=64\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch4hyb_scheduler scheduler.conf perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 499999 perl "threads_per_process=128\\n" . "cpus-per-task=128\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch1phyb_scheduler scheduler.conf perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar < 3000 perl "jobtype=mpi\\n" . "mpi_processes=10\\n" . "threads_per_process=4\\n" . "cpus-per-task=4\\n" . "mem=77G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch2phyb_scheduler scheduler.conf perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 2999 && $nchar < 12000 perl "jobtype=mpi\\n" . "mpi_processes=10\\n" . "threads_per_process=12\\n" . "cpus-per-task=12\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch3phyb_scheduler scheduler.conf perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 11999 && $nchar < 30000 perl "jobtype=mpi\\n" . "mpi_processes=5\\n" . "threads_per_process=25\\n" . "cpus-per-task=25\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch4phyb_scheduler scheduler.conf perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 29999 && $nchar < 200000 perl "jobtype=mpi\\n" . "mpi_processes=2\\n" . "threads_per_process=64\\n" . "cpus-per-task=64\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch5phyb_scheduler scheduler.conf perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 199999 perl "threads_per_process=128\\n" . "cpus-per-task=128\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch perl $specify_workflow eq "FTS" || ($bootstrap_value < 10 && $choose_bootstop ne "bootstop" && $altrun_number < 10) perl "raxmlHPC-PTHREADS_8.2.12_expanse" 0 raxmlhpc_fasttreesearch1_scheduler scheduler.conf perl $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar < 4000 perl "threads_per_process=8\\n" . "cpus-per-task=8\\n" . "mem=15G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch2_scheduler scheduler.conf perl $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 3999 && $nchar < 16000 perl "threads_per_process=16\\n" . "cpus-per-task=16\\n" . "mem=31G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch3_scheduler scheduler.conf perl $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 15999 && $nchar < 60000 perl "threads_per_process=24\\n" . "cpus-per-task=24\\n" . "mem=46G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch4_scheduler scheduler.conf perl $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 59999 && $nchar < 300000 perl "threads_per_process=48\\n" . "cpus-per-task=48\\n" . "mem=92G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch5_scheduler scheduler.conf perl $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 299999 perl "threads_per_process=128\\n" . "cpus-per-task=128\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch1p_scheduler scheduler.conf perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar < 3000 perl "threads_per_process=12\\n" . "cpus-per-task=12\\n" . "mem=23G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch2p_scheduler scheduler.conf perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 2999 && $nchar < 4500 perl "threads_per_process=24\\n" . "cpus-per-task=24\\n" . "mem=46G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch3p_scheduler scheduler.conf perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 4499 && $nchar < 15000 perl "threads_per_process=32\\n" . "cpus-per-task=32\\n" . "mem=61G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch4p_scheduler scheduler.conf perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 14999 && $nchar < 100000 perl "threads_per_process=64\\n" . "cpus-per-task=64\\n" . "mem=120G\\n" . "node_exclusive=0\\n" . "nodes=1\\n" 0 raxmlhpc_fasttreesearch5p_scheduler scheduler.conf perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 99999 perl "threads_per_process=128\\n" . "cpus-per-task=128\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "nodes=1\\n" 0 infile Sequences File (relaxed phylip format) (-s) 1 infile.txt infile_regular perl "-s infile.txt" 1 runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.25 Maximum Hours to Run must be less than 168 perl $runtime > 168.0 Maximum Hours to Run must be greater than 0.1 perl $runtime < 0.1 perl "runhours=$value\\n" The job will run on 40 processors as configured. If it runs for the entire configured time, it will consume 40 x $runtime cpu hours perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar < 10000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 125 x $runtime cpu hours perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 9999 && $nchar < 40000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 39999 && $nchar < 500000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype ne "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 499999 The job will run on 40 processors as configured. If it runs for the entire configured time, it will consume 40 x $runtime cpu hours perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar < 3000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 120 x $runtime cpu hours perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 2999 && $nchar < 12000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 125 x $runtime cpu hours perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 11999 && $nchar < 30000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 29999 && $nchar < 200000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype eq "protein" && $specify_workflow ne "FTS" && ($bootstrap_value > 9 || $choose_bootstop eq "bootstop" || $altrun_number > 9) && $nchar > 199999 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 $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar < 4000 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 $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 3999 && $nchar < 16000 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 $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 15999 && $nchar < 60000 The job will run on 48 processors as configured. If it runs for the entire configured time, it will consume 48 x $runtime cpu hours perl $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 59999 && $nchar < 300000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype ne "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 299999 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 $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar < 3000 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 $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 2999 && $nchar < 4500 The job will run on 32 processors as configured. If it runs for the entire configured time, it will consume 32 x $runtime cpu hours perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 4499 && $nchar < 15000 The job will run on 64 processors as configured. If it runs for the entire configured time, it will consume 64 x $runtime cpu hours perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 14999 && $nchar < 100000 The job will run on 128 processors as configured. If it runs for the entire configured time, it will consume 128 x $runtime cpu hours perl $datatype eq "protein" && (($specify_workflow eq "FTS") || ($bootstrap_value < 10 && $altrun_number < 10 && $choose_bootstop ne "bootstop")) && $nchar > 99999 Estimate the maximum time your job will need to run. We recommend testimg initially with a time less than 0.5hr test run because Jobs set for 0.5 h or less depedendably 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. specify_workflow Select your workflow FTS MLTB BOOTCON MLS FTS Please specify a workflow perl !defined $specify_workflow 1 no_bfgs Don't use BFGS searching algorithm (--no-bfgs) perl $specify_workflow eq "MLTB" || $specify_workflow eq "MLS" || $specify_workflow eq "BOOTCON" 0 10 perl ($value)? "--no-bfgs":"" BFGS is a more efficient optimization algorithm for optimizing branch lengths and GTR parameters simultaneously. You can disable it using this option altrun_number Specify the number alternative runs on distinct starting trees (-#/-N) perl $specify_workflow eq "MLS" || $specify_workflow eq "MLTB" 10 15 Please specify how many runs you wish to execute (must be > 1 ) perl ($specify_workflow eq "MLTB" ||$specify_workflow eq "MLS") && $altrun_number < 2 Sorry, the value for alternative runs must 1000 or less perl ($specify_workflow eq "MLTB" ||$specify_workflow eq "MLS") && $altrun_number > 1000 This option specifies the number of alternative runs on distinct starting trees. For example, if -N 10 is specfied, RAxML will compute 10 distinct ML trees starting from 10 distinct randomized maximum parsimony starting trees. choose_bootstop Specify bootstrap protocol perl $specify_workflow eq "MLTB" || $specify_workflow eq "BOOTCON" specify bootstop specify Please select "Specify an explicit number of bootstraps" or "Let RaxML halt bootstrapping automatically" perl !defined $choose_bootstop Sorry, you can not use a constraint tree with automatic boot stopping perl $choose_bootstop eq "bootstop" && defined $constraint This option instructs Raxml to automatically halt bootstrapping when certain criteria are met, instead of specifying the number of bootstraps for an analysis. The exact criteria are specified/configured using subsequent entry fields. bootstrap_value Bootstrap iterations (-N) perl $choose_bootstop eq "specify" perl " -N $value" 100 2 Please enter number of bootstraps desired (-N) (eg 100) perl $choose_bootstop eq "specify" && !defined $bootstrap_value Sorry, the number of bootstraps must be greater than 1 (-N) perl $bootstrap_value < 2 Sorry, the number of bootstraps cannot exceed 1,000 (-N) perl $bootstrap_value > 1000 Specifies the number of Bootstraps. bootstopping_type Select Bootstopping Criterion: (autoMRE is recommended) perl $choose_bootstop eq "bootstop" perl "-N $value" autoFC autoMR autoMRE autoMRE_IGN autoMRE Please choose a bootstopping criterion perl $choose_bootstop eq "bootstop" && !defined $bootstopping_type printbrlength Print branch lengths (-k) perl ($value)?" -k":"" 0 2 The -k option causes bootstrapped trees to be printed with branch lengths. The bootstraps will require a bit longer to run under this option because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively. fasttree_worklow Fast Tree Search Workflow fasttreesearch_workflow perl $specify_workflow eq "FTS" perl "-f E $clcorrascertainment" 4 outsuffix_FTS Set a name for output files in the FTS workflow perl $specify_workflow eq "FTS" perl "-n $value.tre" infile Please enter a name for Fast Tree Search output files perl $specify_workflow eq "FTS" && !defined $outsuffix_FTS 12 fasttreesearch_workflow2 Optimize model parameters and branch lengths (-f e) perl $specify_workflow eq "FTS" perl ($value) ? "&& raxmlHPC-PTHREADS_8.2.12_expanse -f e -t RAxML_fastTree.$outsuffix_FTS.tre -n brL.$outsuffix_FTS.tre -s infile.txt -O -m $ascertainment$dna_gtrcat$prot_sub_model$bin_model$multi_model$invariable$prot_matrix_spec$use_emp_freq $clcorrascertainment2": "" 0 45 fasttreesearch_workflow3 SH-like values (-f J) perl $specify_workflow eq "FTS" 0 fasttreesearch_optimization perl $fasttreesearch_workflow3 && $fasttreesearch_workflow2 perl "&& raxmlHPC-PTHREADS_8.2.12_expanse -f J -t RAxML_result.brL.$outsuffix_FTS.tre -p $parsimony_seed_val2 -n sh.$outsuffix_FTS.tre -s infile.txt -O -m $ascertainment$dna_gtrcat$prot_sub_model$bin_model$multi_model$invariable$prot_matrix_spec$use_emp_freq $clcorrascertainment3" 0 60 fasttreesearch_nooptimzation perl $fasttreesearch_workflow3 && !$fasttreesearch_workflow2 perl "&& raxmlHPC-PTHREADS_8.2.12_expanse -f J -t RAxML_fastTree.$outsuffix_FTS.tre -p $parsimony_seed_val2 -n sh.$outsuffix_FTS.tre -s infile.txt -O -m $ascertainment$dna_gtrcat$prot_sub_model$bin_model$multi_model$invariable$prot_matrix_spec$use_emp_freq $clcorrascertainment3" 0 60 parsimony_seed_val2 Enter a random seed value for parsimony inferences for the SH- like value step perl $fasttreesearch_workflow3 12345 60 Please enter a random seed for the -p option SH- like value step of the Fast Tree Search workflow (eg 12345) perl $fasttreesearch_workflow3 && !defined $parsimony_seed_val2 MLTB_workflow Maximum Likelihood / Thorough Bootstrap Workflow MLTB_workflow perl $specify_workflow eq "MLTB" perl " -b $mulparambootstrap_seed_val $cloutgroup $clcorrascertainment " 10 mulparambootstrap_seed_val Enter a random seed value for multi-parametric bootstrapping perl $specify_workflow eq "MLTB" 12345 Please enter a random seed for the -b option (eg 12345) perl $mulparambootstrap_seed && !defined $mulparambootstrap_seed_val This random number is provided to assure that there is comparability between runs. outsuffix_MLTB1 Name for output files from the MLTB bootstrapping step perl $specify_workflow eq "MLTB" perl "-n $value" testR 13 Please enter a name for output files from the MLTB bootstrapping step perl $specify_workflow eq "MLTB" && !defined $outsuffix_MLTB1 Sorry, the values for output file names cannot be the same perl $outsuffix_MLTB1 eq $outsuffix_MLTB2 Sorry, the values for output file names cannot be the same perl $outsuffix_MLTB1 eq $outsuffix_MLTB3 Sorry, the values for output file names cannot be the same perl $outsuffix_MLTB2 eq $outsuffix_MLTB3 MLTB_workflow2 perl $specify_workflow eq "MLTB" perl "&& raxmlHPC-PTHREADS_8.2.12_expanse -f d $cloutgroup2 -m $ascertainment$dna_gtrcat$prot_sub_model$bin_model$multi_model$invariable$prot_matrix_spec$use_emp_freqs $clcorrascertainment2 -N $altrun_number -s infile.txt -n $outsuffix_MLTB2 -p $parsimony_seed_val_MLTB2 -O" 30 parsimony_seed_val_MLTB2 Enter a random seed value for MLTB sampling step 12345 45 perl $specify_workflow eq "MLTB" Please enter a random seed for the -p option (eg 12345) perl $specify_workflow eq "MLTB" && !defined $parsimony_seed_val outsuffix_MLTB2 Name for the output files in step 2 of the ML + thorough bootstrap workflow perl $specify_workflow eq "MLTB" testB Please enter a name for the output files for ML + thorough bootstrap workflow step2 perl $specify_workflow eq "MLTB" && !defined $outsuffix_MLTB2 45 no_bfgs2mltb Don't use BFGS searching algorithm (--no-bfgs) && $no_bfgs perl $specify_workflow eq "MLTB" && $no_bfgs 45 perl "--no-bfgs" BFGS is a more efficient optimization algorithm for optimizing branch lengths and GTR parameters simultaneously. You can disable it using this option outsuffix_MLTB3 Set a name for output files in step 3 of the ML Thorough Bootstrapping analysis perl $specify_workflow eq "MLTB" MLTB_output Please enter a name for the MLTB final output files perl $specify_workflow eq "MLTB" && !defined $outsuffix_MLTB3 60 MLTB_workflow3 perl $specify_workflow eq "MLTB" perl "&& raxmlHPC-PTHREADS_8.2.12_expanse -f b -t RAxML_bestTree.$outsuffix_MLTB2 -z RAxML_bootstrap.$outsuffix_MLTB1 -m $ascertainment$dna_gtrcat$prot_sub_model$bin_model$multi_model$invariable$prot_matrix_spec$use_emp_freqs -s infile.txt $clcorrascertainment3 $cloutgroup3 -n $outsuffix_MLTB3 -O" 60 MLS_worklow Maximum Likelihood Search Workflow mlsearch_workflow perl $specify_workflow eq "MLS" perl "-f d -N $altrun_number $clcorrascertainment $no_bfgs" 10 outsuffix_MLS Set a name for output files in the MLS workflow perl $specify_workflow eq "MLS" perl "-n $value.tre" infile Please enter a name for ML Search output files perl $specify_workflow eq "MLS" && !defined $outsuffix_MLS 12 mlsearch_shlike SH-like values (-f J) perl $specify_workflow eq "MLS" 0 mlsearch_combine Combine Results perl $specify_workflow eq "MLS" 0 mlsearch_workflow2 perl $specify_workflow eq "MLS" && $mlsearch_shlike perl "&& raxmlHPC-PTHREADS_8.2.12_expanse -f J -t RAxML_bestTree.$outsuffix_MLS.tre -p $parsimony_seed_val2 -n sh.$outsuffix_MLS.tre -s infile.txt -O -m $ascertainment$dna_gtrcat$prot_sub_model$bin_model$multi_model$invariable$prot_matrix_spec$use_emp_freq $clcorrascertainment2" 0 45 mlsearch_workflow3 perl $specify_workflow eq "MLS" && $mlsearch_combine perl "&& cat RAxML_result.$outsuffix_MLS.tre* > combined_results.$outsuffix_MLS.tre" 0 90 BOOTCON_workflow Rapid Bootstrap / Consensus Tree Workflow BOOTCON_workflow perl $specify_workflow eq "BOOTCON" perl " -x $rapidbootstrap_seed_val $clcorrascertainment $no_bfgs" 12 outsuffix_BOOTCON Set a name for output files from the Rapid Bootstrap Step perl $specify_workflow eq "BOOTCON" perl "-n $value.tre" boot Please enter a name for the output files from the Rapid Bootstrap Step perl $specify_workflow eq "BOOTCON" && !defined $outsuffix_BOOTCON 12 rapidbootstrap_seed_val Enter a random seed value for multi-parametric bootstrapping perl $specify_workflow eq "BOOTCON" 12 12345 Please enter a random seed for the -x option (eg 12345) perl $specify_workflow eq "BOOTCON" && !defined $rapidbootstrap_seed_val This random number is provided to assure that there is comparability between runs. BOOTCON_workflow2 perl $specify_workflow eq "BOOTCON" perl "&& raxmlHPC-PTHREADS_8.2.12_expanse -m $ascertainment$dna_gtrcat$prot_sub_model$bin_model$multi_model$invariable$prot_matrix_spec$use_emp_freqs $clcorrascertainment2 -n $outsuffix_BOOTCON2.tre -J MR -z RAxML_bootstrap.$outsuffix_BOOTCON.tre" 44 outsuffix_BOOTCON2 Name for output files from the Consensus Tree Step perl $specify_workflow eq "BOOTCON" con.tre Please enter a name for output files from the BOOTCON consensus tree step perl $specify_workflow eq "BOOTCON" && !defined $outsuffix_BOOTCON2 Sorry, the output file names cannot be the same perl $outsuffix_BOOTCON2 eq $outsuffix_BOOTCON 50 nchar Enter the number of patterns in your dataset Please enter a value for the number of patterns in your data matrix perl !defined $nchar The number of patterns in the matrix must 1 or greater. perl $nchar < 1 15 Knowing the number of characters in your dataset helps us determine the most efficient way to run raxml. The number of patterns is the number of unique columns in the multiple sequence alignment matrix. You can get this number from the output of the intermediate results once a job begins. Entering the number of characters per taxon in your matirx, or 1000 as the number of patterns is an ok start. Look at the intermediate results, and see if that is reasonably close. If it is not, kill the job, and adjust the number. datatype Please select the Data Type protein dna rna binary multi dna 2 outgroup Outgroup (one or more comma-separated outgroups, see comment for syntax) The correct syntax for the box is outgroup1,outgroup2,outgroupn. If white space is introduced (e.g. outgroup1, outgroup2, outgroupn) the program will fail with the message "Error, you must specify a model of substitution with the '-m' option" cloutgroup perl (defined $outgroup)? "-o $outgroup":"" 12 cloutgroup2 perl (defined $outgroup)? "-o $outgroup":"" 45 cloutgroup3 perl $specify_workflow eq "MLTB" || $specify_workflow eq "FTS" perl (defined $outgroup)? "-o $outgroup":"" 65 number_cats Specify the number of distinct rate categories (-c) perl (defined $value)? " -c $value" : "" 25 2 perl ($datatype eq "dna" && $dna_gtrcat eq "GTRCAT") || ($datatype eq "protein" && $prot_sub_model eq "PROTCAT") || ($datatype eq "binary" && $bin_model eq "BINCAT") This option allows you to specify the number of distinct rate categories, into which the individually optimized rates for each individual site are thrown under -m GTRCAT. The default of -c 25 works fine in most practical cases. treetop Supply a tree (Not available when doing rapid bootstrapping, -x) (-t) perl $specify_workflow ne "BOOTCON" perl " -t tree.tre" 12 tree.tre Specifies a user starting tree file in Newick format. Not available when doing rapid bootstrapping. Branch lengths of that tree will be ignored. Note that you can also specify a non-comprehensive (not containing all taxa in the alignment) starting tree now. This might be useful if newly aligned/sequenced taxa have been added to your alignment. Initially, taxa will be added to the tree using the MP criterion. The comprehensive tree will then be optimized under ML. provide_parsimony_seed Specify a random seed value for parsimony inferences (-p) 1 Please provide a parsimony seed perl $altrun_number > 1 && !defined $parsimony_seed_val Please provide a parsimony seed for the first step of the Fast Tree search workflow perl $specify_workflow eq "FTS" && !defined $parsimony_seed_val Specify a random number seed. The -p option allows you and others to reproduce your results (reproducible/verifiable experiments) and will help Alexis debug the program. Do not use this option if you want to generate multiple different starting trees. parsimony_seed_val Enter a random seed value for parsimony inferences (gives reproducible results from random starting tree) perl ($value) ? " -p $value" : "" 12345 2 perl $provide_parsimony_seed Please enter a random seed for the -p option (eg 12345) perl $provide_parsimony_seed && !defined $parsimony_seed_val constraint perl !defined $binary_backbone && !$use_bootstopping Constraint (-g) constraint.tre perl defined $value ? " -g constraint.tre" : "" 2 This option allows you to specify an incomplete or comprehensive multifurcating constraint tree for the RAxML search in NEWICK format. Initially, multifurcations are resolved randomly. If the tree is incomplete (does not contain all taxa) the remaining taxa are added by using the MP criterion. Once a comprehensive (containing all taxa) bifurcating tree is computed, it is further optimized under ML respecting the given constraints. Important: If you specify a non-comprehensive constraint, e.g., a constraint tree that does not contain all taxa, RAxML will assume that any taxa that not found in the constraint topology are unconstrained, i.e., these taxa can be placed in any part of the tree. As an example consider an alignment with 10 taxa: Loach, Chicken, Human, Cow, Mouse, Whale, Seal, Carp, Rat, Frog. If, for example you would like Loach, Chicken, Human, Cow to be monophyletic you would specify the constraint tree as follows: ((Loach, Chicken, Human, Cow),(Mouse, Whale, Seal, Carp, Rat, Frog)); Moreover, if you would like Loach, Chicken, Human, Cow to be monophyletic and in addition Human, Cow to be monophyletic within that clade you could specify: ((Loach, Chicken, (Human, Cow)),(Mouse, Whale, Seal, Carp, Rat, Frog)); If you specify an incomplete constraint: ((Loach, Chicken, Human, Cow),(Mouse, Whale, Seal, Carp)); the two groups Loach, Chicken, Human, Cow and Mouse, Whale, Seal, Carp will be monophyletic, while Rat and Frog can end up anywhere in the tree. disable_ratehet Disable Rate Heterogeneity (-V) perl ($value)? " -V " : "" 0 2 perl ($datatype eq "dna" && $dna_gtrcat eq "GTRCAT") || ($datatype eq "protein" && $prot_sub_model eq "PROTCAT") || ($datatype eq "binary" && $bin_model eq "BINCAT") This option allows you to disable rate heterogeneity anong the sites. Valid for CAT model only. binary_backbone perl ! defined $constraint Binary Backbone (-r) binary_backbone.tre perl (defined $value) ? " -r binary_backbone.tre" : "" 2 This option allows you to pass a binary/bifurcating constraint/backbone tree in NEWICK format to RAxML. Note that using this option only makes sense if this tree contains fewer taxa than the input alignment. The remaining taxa will initially be added by using the MP criterion. Once a comprehensive tree with all taxa has been obtained it will be optimized under ML respecting the restrictions of the constraint tree. partition Use a mixed/partitioned model? (-q) perl " -q part" 2 part This parameter allows you to upload a file that specifies the regions of your alignment for which an individual model of nucleotide substitution should be estimated. This will typically be used to infer trees for long (in terms of base pairs) multi-gene alignments. If DNA and protein mixed models are used together (for example) you should choose a model option based on the model of rate heterogeneity you want to use. If you specify either -m GTRCAT or PROTCAT, the CAT model will be used, if you specify -m GTRGAMMA or -m BINGAMMA, the GAMMA model will be used .... For example, if -m GTRGAMMA is used, individual alpha-shape parameters, GTR-rates, and empirical base frequencies will be estimated and optimized for each partition. Since Raxml can now handles mixed Amino Acid and DNA alignments, you must specify the data type in the partition file, before the partition name. For DNA, this means you have to add DNA to each line in the partition. For AA data you must specify the transition matrices for each partition: The AA substitution model must be the first entry in each line and must be separated by a comma from the gene name, just like the DNA token above. You can not assign different models of rate heterogeneity to different partitions, i.e. it will be either CAT, GAMMA, GAMMAI etc. for all partitions, as specified with -m. Finally, if you have a concatenated DNA and AA alignments, with DNA data at positions 1 - 500 and AA data at 501-1000 with the WAG model the partition file should look as follows: DNA, gene1 = 1-500 WAG gene2 = 501-1000 ascertainment Correct for Ascertinament bias (ASC_) perl !$invariable ASC_ This is useful for binary/morphological datasets that only contain variable sites (the identical morphological features are usually not included in the alignments, hence you need to correct for this, see, e.g., http://sysbio.oxfordjournals.org/content/50/6/913.short).For DNA data this option might be useful when you analyze alignments of SNPs that also don't contain constant sites. Note that, for mathematical and numerical reasons you can not apply an ascertainment bias correction to datasets or partitions that contain constantsites. In this case, RAxML will exit with an error. corrascertainment Ascertainment bias correction type (--asc-corr) perl $ascertainment lewis felsenstein stamatakis lewis Please specify the ascertainment correction perl $ascertainment && !defined $corrascertainment To use the Felsenstein option, you must specify the number of invariable sites in a file using -q perl $corrascertainment eq "felsenstein" && !defined $partition To use the Stamatakis option, you must specify the number of invariable sites per state for each partition in a file using -q perl $corrascertainment eq "stamatakis" && !defined $partition This option allows to specify the type of ascertainment bias correction you wish to use. There are three types available: Lewis: the standard correction by Paul Lewis, Felsenstein: a correction introduced by Joe Felsenstein that allows to explicitely specify the number of invariable sites (if known) one wants to correct for. Stamatakis: a correction introduced by myself that allows to explicitly specify the number of invariable sites for each character (if known) one wants to correct for. Flesenstein and Stamatkis corrections are accompanied by an upload file specified by the -q option, even if only one partiion is present. For file formatting, please see the RaxML 8.1 or higher manual. clcorrascertainment perl $corrascertainment perl "--asc-corr $corrascertainment" 15 clcorrascertainment2 perl $corrascertainment && ($fasttreesearch_workflow2 || $specify_workflow eq "MLTB" || $mlsearch_shlike || $specify_workflow eq "BOOTCON") perl "--asc-corr $corrascertainment" 45 clcorrascertainment3 perl $corrascertainment && ($fasttreesearch_workflow3 || $specify_workflow eq "MLTB") perl "--asc-corr $corrascertainment" 60 invariable Estimate proportion of invariable sites (GTRGAMMA + I) I The invariable option is not recommended by the developer of RAxML. Please see the manual for details. perl $invariable 2 This option is not recommended by the developer of RAxML exclude_file Choose an input file that excludes the range of positions specifed in this file (-E) perl " -E excl" 2 excl This option is used to excludes specific positions in the matrix. For example, uploading a file that contains the text: 100-200 300-400 will create a file that excludes all columns between positions 100 and 200 as well as all columns between positions 300 and 400. Note that the boundary numbers (positions 100, 200, 300, and 400) will also be excluded. To exclude a single column write (100-100). This option does not run an analysis but just prints an alignment file without the excluded columns. Save this file to your data area, and then run the real analysis. If you use a mixed model, an appropriately adapted model file will also be written. The ntax element of the phylip files is automatically corrected Example: raxmlHPC -E excl -s infile -m GTRCAT -q part -n TEST. In this case the files with columns excluded will be named infile.excl and part.excl. set_weights Weight characters as specifed in this file (-a) perl " -a weights" 2 weights This option alows you to specify a column weight file name to assign individual weights to each column of the alignment. Those weights must be integers separated by any type and number of whitespaces within a separate file. There must, of course, be as many weights as there are columns in your alignment. The contents of an example weight file could look like this: 5 1 1 2 1 1 1 1 1 1 1 2 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 4 1 1 disable_seqcheck Disable checking for sequences with no values (-O) perl ($value) ? "-O" : "" 0 Please use the -O with caution. It disables the check to see if sequences are completely devoid of information. See the RAxML manual for guidance perl $disable_seqcheck 10 nucleic_opts Nucleic Acid Options dna_gtrcat Choose model for bootstrapping phase perl $datatype eq "dna" || $datatype eq "rna" GTRCAT GTRGAMMA perl "-m $ascertainment$dna_gtrcat$invariable" 2 Please choose a DNA model perl ($datatype eq "dna" || $datatype eq "rna") && $dna_gtrcat ne "GTRCAT" && $dna_gtrcat ne "GTRGAMMA" The meaning of the model name GTRGAMMA used by RAxML 7.2.0 is exactly opposite that used in RAxML 7.0.4, so we have eliminated selection by model name. Instead we use a description of the model analysis. This selection gives GTR + Optimization of substitution rates + Optimization of site-specific evolutionary rates which are categorized into "numberOfCategories" distinct rate categories for greater computational efficiency. Final tree is evaluated under GTRGAMMA. GTRMIX and GTRCAT_GAMMA have been eliminated as options. FLOAT options that are native in RAxML 7.2.3 are currently not supported here. The meaning of the model names used by RAxML 7.2.0 are exactly opposite to those used in RAxML 7.0.4, so we have eliminated selection by model name. Instead we use a description of the model analysis. This option gives GTR + Optimization of substitution rates + GAMMA model of rate heterogeneity (alpha parameter will be estimated) for bootstrap AND final evaluation. An analysis run in this way will take a good deal longer than the alternative option (what used to be called GTRGAMMA in RAxML v.7.0.4). GTRMIX and GTRCAT_GAMMA have been eliminated as options. FLOAT options that are native in RAxML 7.2.3 are currently not supported here. protein_opts Protein Analysis Options prot_sub_model Choose GAMMA or CAT model: perl $datatype eq "protein" PROTGAMMA PROTCAT perl "-m $ascertainment$prot_sub_model$invariable$prot_matrix_spec$use_emp_freqs" 2 Please choose a protein model perl $datatype eq "protein" && $prot_sub_model ne "PROTGAMMA" && $prot_sub_model ne "PROTCAT" prot_matrix_spec Protein Substitution Matrix perl $datatype eq "protein" DAYHOFF DCMUT JTT MTREV WAG RTREV CPREV VT BLOSUM62 MTMAM LG MTART MTZOA PMB HIVB HIVW JTTDCMUT FLU DUMMY DUMMY2 AUTO LG4M LG4X PROT_FILE GTR_UNLINKED GTR Note: FLOAT and invariable sites (I) options are not exposed here. If you require this option, please contact mmiller@sdsc.edu. -m PROTCATmatrixName: analyses using the specified AA matrix + Optimization of substitution rates + Optimization of site-specific evolutionary rates which are categorized into numberOfCategories distinct rate categories for greater computational efficiency. Final tree might be evaluated automatically under PROTGAMMAmatrixName[f], depending on the tree search option. -m PROTGAMMAmatrixName[F] analyses use the specified AA matrix + Optimization of substitution rates + GAMMA model of rate heterogeneity (alpha parameter will be estimated) Available AA substitution models: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG, GTR. You can specify if you want to use empirical base frequencies. Please note that for mixed models you can in addition specify the per-gene AA model in the mixed model file (see manual for details). Also note that if you estimate AA GTR parameters on a partitioned dataset, they will be linked (estimated jointly) across all partitions to avoid over-parametrization. user_prot_matrix Upload a Custom Protein Substitution Matrix perl $datatype eq "protein" perl "-P Userproteinmatrix.txt" 2 Userproteinmatrix.txt Specify a file containing a user-defined Protein substitution model. This file must contain 420 entries, the first 400 entires are the AA substitution rates (this matrix must be symmetric) and the last 20 entries are the empirical base frequencies mulcustom_aa_matrices Use a Partition file that specifies AA Matrices perl $datatype eq "protein" Please choose a partition file specifying up to 5 partitions perl $mulcustom_aa_matrices && !defined $partition This option can be used to specify multiple custom matrices via a partition file. The filenames must be specified as firstpartition, secondpartition, thirdpartition, fourthpartition, and fifthpartition, in order, user_prot_matrixq1 Select the First Protein Substitution Matrix Called in Your Partition File perl $mulcustom_aa_matrices firstpartition This option allows the user to upload a Protein subsitution matrix user_prot_matrixq2 Select the Second Protein Substitution Matrix Called in Your Partition File perl $mulcustom_aa_matrices && defined $user_prot_matrixq1 secondpartition This option allows the user to upload a second Protein subsitution matrix user_prot_matrixq3 Select the Third Protein Substitution Matrix Called in Your Partition File perl $mulcustom_aa_matrices && defined $user_prot_matrixq2 thirdpartition This option allows the user to upload a third Protein subsitution matrix user_prot_matrixq4 Select the Fourth Protein Substitution Matrix Called in Your Partition File perl $mulcustom_aa_matrices && defined $user_prot_matrixq3 fourthpartition This option allows the user to upload a fourth Protein subsitution matrix user_prot_matrixq5 Select the Fifth Protein Substitution Matrix Called in Your Partition File perl $mulcustom_aa_matrices && defined $user_prot_matrixq4 fifthpartition This option allows the user to upload a fifth Protein subsitution matrix use_emp_freqs Use empirical frequencies? perl $datatype eq "protein" F Sec_structure_opts RNA Secondary Structure Options sec_str_file perl $datatype eq "rna" Upload a Secondary Structure File (-S) sec_structure.txt perl (defined $value) ? " -S sec_structure.txt" : "" 2 This option allows you to provide a secondary structure file. The file can contain "." for alignment columns that do not form part of a stem and characters, while "(), [], and {}" are used to define stem regions and pseudoknots. rna_model Use an RNA Secondary Structure Substitution Model (-A) perl defined $sec_str_file S6A S6B S6C S6D S6E S7A S7B S7C S7D S7E S7F S16A S16B S16A perl "-A $value" 2 Use this option to specify one of the 6, 7, or 16 state RNA secondary structure substitution models.The nomenclature is identical to that used in the program PHASE. For more information, see PHASE documentation: 6 state model nomenclature: http://www.cs.manchester.ac.uk/ai/Software/phase/manual/node101.html; 7 state model nomenclature http://www.cs.manchester.ac.uk/ai/Software/phase/manual/node107.html; 16 state model nomenclature http://www.cs.manchester.ac.uk/ai/Software/phase/manual/node114.html bin_opts Binary Matrix Options bin_model Binary data model (-m) perl $datatype eq "binary" BINCAT BINGAMMA perl "-m $ascertainment$bin_model$invariable" 2 Please choose a binary model perl $datatype eq "binary" && $bin_model ne "BINCAT" && $bin_model ne "BINGAMMA" Binary data is handled in RAXML 7.2.0. Binary CAT use optimization of site-specific evolutionary rates, which are categorized into numberOfCategories (option -c) distinct rate categories for greater computational efficiency. Final tree might be evaluatedautomatically under BINGAMMA, depending on the tree search option. Binary GAMMA uses the GAMMA model of rate heterogeneity (alpha parameter will be estimated). The option for invariable sites is not provided at this time. The program's author supports the use of Gamma models. multi_opts Multiple State Morphological Matrix Options multi_model Multiple State Data Model (-m) perl $datatype eq "multi" MULTICAT MULTIGAMMA perl "-m $ascertainment$value$invariable" 2 Please choose a Multi-State model perl $datatype eq "multi" && $multi_model ne "MULTICAT" && $multi_model ne "MULTIGAMMA" Multi-state morphological data are handled in RAXML at V. 7.3.0 and above. Multi-state CAT uses optimization of site-specific evolutionary rates which are categorized into numberOfCategories distinct rate categories for greater computational efficiency. Final tree might be evaluated automatically under MULTIGAMMA depending on the tree search option Mutli-state GAMMA uses the GAMMA model of rate heterogeneity (alpha parameter will be estimated). Invariable sites (I) options are not exposed here. If you require this option, please contact mmiller@sdsc.edu. choose_multi_model Select a Multiple state data model (-K) perl $datatype eq "multi" ORDERED MK GTR GTR perl "-K $value" 2 Please choose a Multi-State data model perl $datatype eq "multi" && $choose_multi_model ne "ORDERED" && $choose_multi_model ne "MK" && $choose_multi_model ne "GTR" Multi-state morphological data are handled in RAXML 7.3.0 and above. Multi-state CAT uses optimization of site-specific evolutionary rates which are categorized into numberOfCategories distinct rate categories for greater computational efficiency. Final tree might be evaluated automatically under MULTIGAMMA depending on the tree search option Mutli-state GAMMA uses the GAMMA model of rate heterogeneity (alpha parameter will be estimated). The program's author supports the use of Gamma models. all_outputfiles *