2.02 Accurate detection of unreliable alignment regions - run on XSEDE. Phylogeny / Alignment guidance2_xsede invocation_string 0 perl "guidance2_expanse_2.0.2" infile Alignment or sequence file (phylip) 2 infile.phy infile_msa Sequence file (phylip) 1 perl "--seqFile infile.phy" output_string 99 perl "--outDir ./" onenode 1 scheduler.conf perl "nodes=1 \\n" cores_used 1 scheduler.conf perl "mem=" . (int($specify_procnum*(248/32))) . "G\\n" . "threads_per_process=$specify_procnum\\n" node_exclusive 1 scheduler.conf perl "node_exclusive=0\\n" all_results * runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.5 Maximum Hours to Run must be between 0.1 - 168.0. perl $runtime < 0.1 || $runtime > 168.0 The job will run on $specify_procnum processors as configured. If it runs for the entire configured time, it will consume $specify_procnum X $runtime cpu hours perl defined $runtime perl "runhours=$value\\n" Estimate the maximum time your job will need to run. We recommend testimg initially with a < 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. use_msafile My Input file is a sequence alignment (--msaFile) 7 select_program Select program (--program) 3 GUIDANCE GUIDANCE GUIDANCE2 GUIDANCE2 HoT HoT perl (defined $value) ? "--program $value":"" select_msaprogram Select the MSA program that created your dataset (--msaProgram) 3 MAFFT MAFFT CLUSTALW CLUSTALW MUSCLE MUSCLE perl (defined $value) ? "--msaProgram $value":"" Sorry you cant use MUSCLE with Guidance2, use Guidance instead perl $select_msaprogram eq "MUSCLE" && $select_program eq "GUIDANCE2" Sorry you cant use PAGAN with Guidance2, use Guidance instead perl $select_msaprogram eq "PAGAN" && $select_program eq "GUIDANCE2" select_seqtype Select the Sequence type (-seqType) 3 aa Amino Acid nuc Nucleotide codon Codon perl (defined $value) ? "-seqType $value":"" specify_bootstraps Specify the number of bootstraps (--bootstraps) 3 perl (defined $value) ? "--bootstraps $value":"" 100 specify_geneticcode Specify the Genetic Code (--genCode) 3 perl $select_seqtype eq "codon" 1 Nuclear Standard 15 Nuclear Blepharisma 6 Nuclear Ciliate 10 Nuclear Euplotid 2 Mitochondria Vertebrate 5 Mitochondria Invertebrate 3 Mitochondria Yeast 13 Mitochondria Ascidian 9 Mitochondria Echinoderm 14 Mitochondria Flatworm 4 Mitochondria Protozoan perl (defined $value) ? "--genCode $value":"" 1 specify_seqcutoff Sequence Confidence cutoff (default is 0.6) 3 perl (defined $value) ? "--seqCutoff $value":"" 0.6 The confidence cutoff must be between 0 and 1 perl $value >= 1 && $value <= 0 specify_colcutoff Column Confidence cutoff (default is 0.93) 3 perl (defined $value) ? "--colCutoff $value":"" 0.93 The confidence cutoff must be between 0 and 1 perl $value >= 1 && $value <= 0 specify_msaparam Pass a parameter to the alignment program (-F for PRANK) 6 perl (defined $value) ? "--MSA_Param \/$value ":"" specify_procnum Number of processors (--proc_num). Max 12. 3 perl (defined $value) ? "--proc_num $value":"" 1 specify_outorder Output order = Input Order (default is aligned) 3 perl ($value) ? "--outOrder as_input":"" 0