POY 4.1.2 Phylogenetic tree inference using dynamic homologies. Andres Varon, Le Sy Vinh, Illya Bomash, and Ward Wheeler Varon, A., L. S. Vinh, W. C.Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics. 26: in press. Phylogeny / Alignment http://research.amnh.org/scicomp/projects/poy.php poy scheduler_input scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "node_exclusive=0\\n" . "threads_per_process=1\\n" runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 1.0 Estimate the maximum time your job will need to run (up to 72 hrs). Your job will be killed if it doesn't finish within the time you specify, however jobs with shorter maximum run times are often scheduled sooner than longer jobs. Maximum Hours to Run must be between 0.1 - 72.0. perl $runtime < 0.1 || $runtime > 72.0 Please set a value for the runtime perl !defined $runtime perl "runhours=$value\\n" poy_server perl "poy_server_4.1.2" 0 infile Input File perl " -input infile" 1 infile All files that could be accepted in the command read ("file") are acceptable input in this field, that includes (but is not limited to) FASTA, NEXUS, Hennig (TNT/NONA), and Newick tree formats. Aminoacid files or custom alphabet definitions (for example for locus sequences), are currently not supported in the portal. infile2 Input File perl " -input infile2" 1 infile2 infile3 Input File perl " -input infile3" 1 infile3 infile4 Input File perl " -input infile4" 1 infile4 infile5 Input File perl " -input infile5" 1 infile5 infile6 Input File perl " -input infile6" 1 infile6 substitutions Substitution cost perl ($value && $value > 0) ? " -substitutions $value" : "" 1 1 indels Individual insertion and deletion cost perl ($value && $value > 0) ? " -indels $value" : "" 1 1 gapopening Gap opening cost perl ($value && $value > (-1)) ? " -gapopening $value" : "" 0 1 terminalsfile Terminals file perl " -terminals terminalsfile" 1 terminalsfile File containing the list of terminals appearing in the input files that should be included in the analysis. One terminal per line. synonyms Synonyms file perl " -synonyms synonymsfile" 1 synonymsfile A synonyms file is useful to quickly map names of terminals that are different in various files to a unique name, or to the name that the user wants for publication. For example, each input file could be a FASTA format with the Genbank accession number as terminal name. In this way, a Chicken with 3 genes in the data set could appear as AF1 in File1, BC2 in File2, and CX3 in File3, while the corresponding Human genes appear as XB1, YR4, and ZE3. To recognize them all as Chicken, and Human genes, it is sufficient to provide a synonym file with the following 2 lines: Chicken AF1 BC2 CX3 Human XB1 YR4 ZE3 There should be one line for each set of terminals in the input file that should be synonyms of a single resulting terminal. outgroup Outgroup perl (defined $value)? " -outgroup '$value'" : "" 2 constraint Constraint tree constraint.file perl defined $value ? " -constraint constraint.file" : "" 2 A constraint file contains a tree with all the terminals contained in the input files (or the terminals file if it is selected), that POY should respect during the search. That is, all the binary trees that POY evaluate must be resolutions of the polytomies defined in the constraint file. The file format could be any of the tree formats read by POY (e.g. newick). For example, if the file contains (A B C (D E)) then the trees (A (B (C (D E)))), ((A (B C)) (D E)) would be alowed during the search, but ((A D) ((B C) E)) as D and E are not sister terminals. randomseed Random seed for the program initialization. perl ($value) ? " -randomseed $value" : "" 2 supportparagraph Support calculation (require input tree) 2 support Support calculation (requires a tree in one of the input files) bremer jackknife bootstrap perl " -support $value" 2 pseudoreplicates Number of pseudoreplicates for bootstrap and jakknife perl $support eq "jackknife" || $support eq "bootstrap" 2 perl ($value && $value > 0) ? " -pseudoreplicates $value" : "" remove Percentage of characters to be removed per pseudoreplicate during jackknife perl $support eq "jackknife" 2 perl ($value && $value > 0) ? " -remove $value" : "" all_results *