CLANN 4.2.5 Software for inferring phylogenetic supertrees C. J. Creevey and J. O. McInerney Creevey C. J. and McInerney, J. O. (2005) Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21 (3): 390-2. Phylogeny / Alignment http://mcinerneylab.com/software/clann/ clann_expanse invoke_clann perl "clann_4.2.5_expanse" 0 scheduler_input scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=243G\\n" . "node_exclusive=1\\n" . "threads_per_process=1\\n" commands_header perl $nexusBlock == 2 && !defined $commandfile_mine commandfile.txt perl "# This is a commands file for use in a CIPRES application\\n" . "# For use of a commands file in clann\\n" . "# This file is run by calling clann as follows:\\n" . "# clann -c commandfile.txt\\n" 1 infile infile.tre commandfile_command perl $nexusBlock == 2 perl "-c commandfile.txt" 10 clann_invoke1 perl $nexusBlock == 2 && !defined $commandfile_mine && !defined $specify_maxnamelen && !defined $specify_delimiter perl "# Start with invocation followed by the tree file:\\n" . "exe infile.tre\\n" . " \\n" commandfile.txt 1 clann_invoke2 perl $nexusBlock == 2 && !defined $commandfile_mine && defined $specify_maxnamelen && !defined $specify_delimiter perl "# Start with invocation followed by the tree file:\\n" . "exe infile.tre -maxnamelen=$specify_maxnamelen \\n" . " \\n" commandfile.txt 1 clann_invoke3 perl $nexusBlock == 2 && !defined $commandfile_mine && !defined $specify_maxnamelen && defined $specify_delimiter perl "# Start with invocation followed by the tree file:\\n" . "exe infile.tre -delimiter_char $specify_delimiter\\n" . "\\n" commandfile.txt 1 clann_invoke4 perl $nexusBlock == 2 && !defined $commandfile_mine && defined $specify_maxnamelen && defined $specify_delimiter perl "# Start with invocation followed by the tree file:\\n" . "exe infile.tre -maxnamelen= $specify_maxnamelen -delimiter_char $specify_delimiter\\n" . "\\n" commandfile.txt 1 suptreerecon_hscommand perl $specify_start ne "user" && $specify_suptreerecon eq "hs" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a heuristic search supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps weight=$specify_weighttype savetrees=$specify_outputname drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_hscommand1b perl $specify_start ne "user" && $specify_suptreerecon eq "hs" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a heuristic search supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps weight=$specify_weighttype savetrees=$specify_outputname analysis=parsimony drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_hscommand1c perl $specify_start ne "user" && $specify_suptreerecon eq "hs" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a heuristic search supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps weight=$specify_weighttype savetrees=$specify_outputname analysis=nj drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_commandhs2 perl $specify_start eq "user" && $specify_suptreerecon eq "hs" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a heuristic search supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps savetrees=$specify_outputname weight=$specify_weighttype drawhistogram=yes nbins=20 ;\\n" . " \\n" commandfile.txt suptreerecon_hscommand2b perl $specify_start ne "user" && $specify_suptreerecon eq "hs" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a heuristic search supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps weight=$specify_weighttype savetrees=$specify_outputname analysis=parsimony drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_hscommand2c perl $specify_start ne "user" && $specify_suptreerecon eq "hs" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a heuristic search supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps weight=$specify_weighttype savetrees=$specify_outputname analysis=nj drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_bscommand1 perl $specify_suptreerecon eq "bootstrap" && $specify_start ne "user" && $specify_consensus ne "user" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a bootstrap supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps consensus=$specify_consensus weight=$specify_weighttype treefile=$specify_outputname drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_bscommand1b perl $specify_suptreerecon eq "bootstrap" && $specify_start ne "user" && $specify_consensus ne "user" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a bootstrap supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps consensus=$specify_consensus weight=$specify_weighttype analysis=parsimony treefile=$specify_outputname drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_bscommand1c perl $specify_suptreerecon eq "bootstrap" && $specify_start ne "user" && $specify_consensus ne "user" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a bootstrap supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps consensus=$specify_consensus weight=$specify_weighttype treefile=$specify_outputname analysis=nj tdrawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_commandbootstrap2 perl $specify_suptreerecon eq "bootstrap" && $specify_start eq "user" && $specify_consensus ne "user" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a bootstrap supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensus treefile=$specify_outputname drawhistogram=yes nbins=20 ;\\n" . " \\n" commandfile.txt suptreerecon_commandbootstrap2b perl $specify_suptreerecon eq "bootstrap" && $specify_start eq "user" && $specify_consensus ne "user" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a bootstrap supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensus treefile=$specify_outputname analysis=parsimony drawhistogram=yes nbins=20 ;\\n" . " \\n" commandfile.txt suptreerecon_commandbootstrap2c perl $specify_suptreerecon eq "bootstrap" && $specify_start eq "user" && $specify_consensus ne "user" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a bootstrap supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensus treefile=$specify_outputname analysis=nj drawhistogram=yes nbins=20 ;\\n" . " \\n" commandfile.txt suptreerecon_bscommand3 perl $specify_suptreerecon eq "bootstrap" && $specify_start ne "user" && $specify_consensus eq "user" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a bootstrap supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensusfr treefile=$specify_outputname drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_bscommand3b perl $specify_suptreerecon eq "bootstrap" && $specify_start ne "user" && $specify_consensus eq "user" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a bootstrap supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensusfr treefile=$specify_outputname drawhistogram=yes analysis=parsimony nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_bscommand3c perl $specify_suptreerecon eq "bootstrap" && $specify_start ne "user" && $specify_consensus eq "user" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a bootstrap supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensusfr treefile=$specify_outputname drawhistogram=yes analysis=nj nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_commandbootstrap4 perl $specify_suptreerecon eq "bootstrap" && $specify_start eq "user" && $specify_consensus eq "user" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a bootstrap supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensusfr treefile=$specify_outputname drawhistogram=yes nbins=20 ;\\n" . " \\n" commandfile.txt suptreerecon_commandbootstrap4b perl $specify_suptreerecon eq "bootstrap" && $specify_start eq "user" && $specify_consensus eq "user" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a bootstrap supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensusfr treefile=$specify_outputname analysis=parsimony drawhistogram=yes nbins=20 ;\\n" . " \\n" commandfile.txt suptreerecon_commandbootstrap4c perl $specify_suptreerecon eq "bootstrap" && $specify_start eq "user" && $specify_consensus eq "user" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a bootstrap supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps swap=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps weight=$specify_weighttype consensus=$specify_consensusfr treefile=$specify_outputname analysis=nj drawhistogram=yes nbins=20 ;\\n" . " \\n" commandfile.txt suptreerecon_yaptpcommand perl $specify_start ne "user" && $specify_suptreerecon eq "yaptp" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a yaptp supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps search=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps method=$specify_method weight=$specify_weighttype treefile=$specify_outputname drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_yaptpcommand1b perl $specify_start ne "user" && $specify_suptreerecon eq "yaptp" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a yaptp supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps search=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps method=$specify_method weight=$specify_weighttype treefile=$specify_outputname analysis=parsimony drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_yaptpcommand1c perl $specify_start ne "user" && $specify_suptreerecon eq "yaptp" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a yaptp supertree \\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps search=$specify_swap nsteps=$specify_nsteps start=$specify_start maxswaps=$specify_maxswaps hsreps=$specify_hsreps method=$specify_method weight=$specify_weighttype treefile=$specify_outputname analysis=nj drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_yaptpcommandhs2 perl $specify_start eq "user" && $specify_suptreerecon eq "yaptp" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a yaptp supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps search=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps method=$specify_method weight=$specify_weighttype treefile=$specify_outputname drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_yaptpcommandhs2b perl $specify_start eq "user" && $specify_suptreerecon eq "yaptp" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a yaptp supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps search=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps method=$specify_method weight=$specify_weighttype treefile=$specify_outputname analysis=parsimony drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_yaptpcommandhs2c perl $specify_start eq "user" && $specify_suptreerecon eq "yaptp" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a yaptp supertree with a user provided starting tree\\n" . "$specify_suptreerecon sample=$specify_sampleno nreps=$specify_nreps search=$specify_swap nsteps=$specify_nsteps start=startingtree.tre maxswaps=$specify_maxswaps hsreps=$specify_hsreps method=$specify_method weight=$specify_weighttype treefile=$specify_outputname analysis=nj drawhistogram=yes nbins=20;\\n" . " \\n" commandfile.txt suptreerecon_njcommand perl $specify_suptreerecon eq "nj" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a neighbor joining supertree \\n" . "$specify_suptreerecon missing=$specify_missingdata savetrees=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_njcommand1b perl $specify_suptreerecon eq "nj" && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a neighbor joining supertree \\n" . "$specify_suptreerecon missing=$specify_missingdata savetrees=$specify_outputname analysis=parsimony;\\n" . " \\n" commandfile.txt suptreerecon_njcommand1c perl $specify_suptreerecon eq "nj" && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a neighbor joining supertree \\n" . "$specify_suptreerecon missing=$specify_missingdata savetrees=$specify_outputname analysis=nj;\\n" . " \\n" commandfile.txt suptreerecon_alltreescommand perl $specify_suptreerecon eq "alltrees" && !defined $specify_range && $specify_criterion ne "mrp" 20 perl "#instructions to build a build an alltrees supertree \\n" . "$specify_suptreerecon create=$specify_create weight=$specify_weighttype savetrees=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_alltreescommand1b perl $specify_suptreerecon eq "alltrees" && !defined $specify_range && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build an alltrees supertree \\n" . "$specify_suptreerecon create=$specify_create weight=$specify_weighttype savetrees=$specify_outputname analysis=parsimony;\\n" . " \\n" commandfile.txt suptreerecon_alltreescommand1c perl $specify_suptreerecon eq "alltrees" && !defined $specify_range && $specify_parsornj eq "nj" 20 perl "#instructions to build a build an alltrees supertree \\n" . "$specify_suptreerecon create=$specify_create weight=$specify_weighttype savetrees=$specify_outputname analysis=nj;\\n" . " \\n" commandfile.txt suptreerecon_alltreescommand2 perl $specify_suptreerecon eq "alltrees" && defined $specify_range && $specify_criterion ne "mrp" 20 perl "#instructions to build a build an alltrees supertree \\n" . "$specify_suptreerecon range=$specify_range create=$specify_create weight=$specify_weighttype savetrees=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_alltreescommand2b perl $specify_suptreerecon eq "alltrees" && defined $specify_range && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build an alltrees supertree \\n" . "$specify_suptreerecon range=$specify_range create=$specify_create weight=$specify_weighttype savetrees=$specify_outputname analysis=parsimony;\\n" . " \\n" commandfile.txt suptreerecon_alltreescommand2c perl $specify_suptreerecon eq "alltrees" && defined $specify_range && $specify_parsornj eq "nj" 20 perl "#instructions to build a build an alltrees supertree \\n" . "$specify_suptreerecon range=$specify_range create=$specify_create weight=$specify_weighttype savetrees=$specify_outputname analysis=nj;\\n" . " \\n" commandfile.txt suptreerecon_usertreescommand perl $specify_suptreerecon eq "usertrees" && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a usertree supertree \\n" . "$specify_suptreerecon usertrees.txt weight=$specify_weighttype printsourcescores=$specify_printscores outfile=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand perl $specify_suptreerecon eq "consensus" && $specify_consensus ne "user" && !defined $consensus_guidetree && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensus filename=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand1b perl $specify_suptreerecon eq "consensus" && $specify_consensus ne "user" && !defined $consensus_guidetree && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensus filename=$specify_outputname analysis=parsimony;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand1c perl $specify_suptreerecon eq "consensus" && $specify_consensus ne "user" && !defined $consensus_guidetree && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensus filename=$specify_outputname analysis=nj;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand2 perl $specify_suptreerecon eq "consensus" && $specify_consensus eq "user" && !defined $consensus_guidetree && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensusfr filename=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand2b perl $specify_suptreerecon eq "consensus" && $specify_consensus eq "user" && !defined $consensus_guidetree && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensusfr filename=$specify_outputname analysis=parsimony;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand2b perl $specify_suptreerecon eq "consensus" && $specify_consensus eq "user" && !defined $consensus_guidetree && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensusfr filename=$specify_outputname analysis=nj;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand3 perl $specify_suptreerecon eq "consensus" && $specify_consensus ne "user" && defined $consensus_guidetree && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensus guidetree=guidetree.tre filename=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand3b perl $specify_suptreerecon eq "consensus" && $specify_consensus ne "user" && defined $consensus_guidetree && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensus guidetree=guidetree.tre analysis=parsimony filename=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand3c perl $specify_suptreerecon eq "consensus" && $specify_consensus ne "user" && defined $consensus_guidetree && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensus guidetree=guidetree.tre analysis=nj filename=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand4 perl $specify_suptreerecon eq "consensus" && $specify_consensus eq "user" && defined $consensus_guidetree && $specify_criterion ne "mrp" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensusfr guidetree=guidetree.tre filename=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand4b perl $specify_suptreerecon eq "consensus" && $specify_consensus eq "user" && defined $consensus_guidetree && $specify_parsornj eq "parsimony" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensusfr guidetree=guidetree.tre analysis=parsimony filename=$specify_outputname;\\n" . " \\n" commandfile.txt suptreerecon_consensuscommand4c perl $specify_suptreerecon eq "consensus" && $specify_consensus eq "user" && defined $consensus_guidetree && $specify_parsornj eq "nj" 20 perl "#instructions to build a build a consensus supertree \\n" . "$specify_suptreerecon method=$specify_consensusfr guidetree=guidetree.tre analysis=nj filename=$specify_outputname;\\n" . " \\n" commandfile.txt quit_command 90 perl "#here is the quit command \\n" . "quit;\\n" . " \\n" commandfile.txt runtime Maximum Hours to Run (click here for help setting this correctly) 1 scheduler.conf perl "runhours=$value\\n" 1.0 Maximum Hours to Run must be between 0.1 - 168.0. perl $runtime < 0.1 || $runtime >168.0 Please enter a value for the runtime perl !defined $runtime Your job will run on one processor as configured. If it runs for the full specificed time, it will consume 1x $runtime cpu hours perl defined $runtime 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. specify_maxnamelen Consider only the first x letters of each taxon name. This option allows the user to specify that the software should only look at the first x number of characters when reading the taxon name. This allows the inclusion of other information along with the name of the taxa. nexusBlock Data set is in Nexus format, and has a Clann block 1 2 Please specify whether or not you have a Clann Nexus block in your input file perl !defined $nexusBlock Clann receives instructions either from commands you specify in the interface below, or from a CLANN block in your input file (Nexus format). Either option is fine, but you must specify which method you are using. If you specified the run paramters in a Clann Nexus block, you must specify it here, or the run will fail. commandfile_mine Provide your own command file commandfile.txt perl $nexusBlock == 2 If you reate your own command file, the input tree file read into memory must be named infile.tre perl defined $commandfile_mine You can select your own Clann command file here. specify_criterion Specify your criterion (set -criterion) perl $nexusBlock == 2 && !defined $commandfile_mine dfit sfit qfit mrp avcon Please select a criterion for your analysis perl !defined $specify_criterion specify_outputname Specify an output name perl $nexusBlock == 2 && !defined $commandfile_mine Please enter a name for the output file perl !defined $specify_outputname specify_seed Specify a seed (set -seed) perl $nexusBlock == 2 && !defined $commandfile_mine specify_criterionhidden perl $specify_analysis == 1 5 perl "#instructions to specify the search criterion\\n" . "set criterion=$specify_criterion;\\n" . " \\n" commandfile.txt specify_seedhidden perl $specify_analysis == 1 && defined $specify_seed 5 perl "#instructions to specify the seed\\n" . "set seed=$specify_seed;\\n" . " \\n" commandfile.txt specify_analysis What analysis do you wish to run? perl $nexusBlock == 2 && !defined $commandfile_mine 1 2 3 4 Please specify which analysis you wish to run perl !defined $specify_analysis supertree_recon Supertree Reconstruction specify_suptreerecon What Supertree reconstruction method? perl $specify_analysis == 1 hs bootstrap yaptp nj alltrees usertrees consensus Please select a method for the supertree reconstruction perl !defined $specify_suptreerecon You cannot do a usertree search under MRP criterion perl $specify_suptreerecon eq "usertrees" && $specify_criterion eq "mrp" You cannot do a usertree search under AVCON criterion perl $specify_suptreerecon eq "usertrees" && $specify_criterion eq "avcon" 1 Heuristic search: Carry out a heuristic search for the best supertree usign the criterion selected; Bootstrap - Carry out a bootstrap supertree analysis using the criterion selected NeighborJoining - Construct a neighbour-joining supertree; Alltrees - Exhaustively search all possible supertrees; Usertrees - Assess user-defined supertrees (from seperate file), to find the best scoring Consensus - Calculate a consensus tree of all trees containing all taxa specify_start Specify the starting tree method perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap") nj random user nj Please specify your starting tree method perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap") && !defined $specify_start By default, the heuristic search starts with a neighbor-joining tree calculated from average consensus distances (with missing distances estimated using either ultrametric or 4-point condition distances). If more than one repetition of the heuristic search is to be carried out, the first repetition uses the nj tree as a starting point and every subsequent repetition uses the nj tree after a randomly chosen number of SPR operations having been carried out on it. If the user decides to use a randomly chsen tree as a starting point for the heuristic search, a certain number of random trees are evaluated (specified by the option sample) and the top few are retained (the number of which is specified by the option nreps). These top trees are then used as starting points for each of the repetitions of the heuristic search. Finally, it is possible to specify a filename that contains trees which are to be used as starting points If any other word other than nj or random is placed after the option start, it is assumed that this is the name of a file containing starting trees. This overrides the options sample and nreps . i.e. start=random or start=mytrees.txt specify_startfile Select your starting tree file perl $specify_start eq "user" startingtree.tre Please select a starting tree file perl $specify_start eq "user" && !defined $specify_start specify_sampleno Number of supertrees to be evaluated before search (-sample) perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") 10000 Please specify the number of supertrees to be evalauted perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") && !defined $specify_sampleno This option determines the number of randomly chosen supertrees are evaluated before heuristic searches are carried out. The top x number of trees are kept as starting points for each of the x repetitions of the heuristic search. The default value is 10,000. specify_nreps Number of reptitions or bootstraps (-nreps) perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") 10 Please specify the number of repitions or bootstraps perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") && !defined $specify_nreps This option specifies the number of repetitions of the heuristic search or the number of bootstrap reps that are to be carried out. The best tree found is picked from all the repetitions carried out. specify_swap Heuristic search type (-swap or -search) perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") nni spr tbr all spr Please specify the search or swap type perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") && !defined $specify_swap Tbr is not valid for Yaptp Search Option (search=yaptp) perl $specify_swaps eq "tbr" && $specify_suptreerecon eq "yaptp" All is not valid only for the Heuristic Search Option (swap=hs) perl $specify_swaps eq "all" && $specify_suptreerecon eq "hs" All is not valid only for the MRP criterion (criterion=MRP) perl $specify_swaps eq "all" && $specify_criterion eq "mrp" This option determines the type of heuristic search that is to be carried out. nni specifies that the nearest neighbor interchange method is to be used spr specifies that the sub tree pruning and regrafting method is to be used. specify_nsteps Maximum number of steps from original position (-nsteps) perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp" ) 3 Please specify the maximum number of steps allowed perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp" ) && !defined $specify_nsteps This option specifies the maximum number of steps away from its original position that any branch may be swapped or regrafted. The default value is 3. specify_maxswaps Maximum number of swaps/rearrangements (-maxswap) perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") 1000000 Please specify the maximum number of steps allowed perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp" ) && !defined $specify_maxswaps This option specifies the maximum number of swaps/rearrangements to be tried during the search. This is set to 1,000,000 by default, but some searches may take too long so it may be desirable to set a lower limit. The number of random samples carried out before the heuristic searches are not counted for the maxswaps limitation specify_hsreps Maximum number of repetitions of the heuristic search (-hsreps) perl ($specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") 10 Please specify the maximum number of repititions allowed perl ($specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "yaptp") && !defined $specify_hsreps The maximum number of supertrees sampled must be greater than the value of hsreps perl $specify_sampleno < $specify_hsreps This option defines how many repetitions of the heuristic search are to be carried out on each bootstrap or YAPTP replicate. specify_weighttype Weight used to normalise the scoring system (-weight) perl ($specify_suptreerecon eq "hs" || $specify_suptreerecon eq "bootstrap" || $specify_suptreerecon eq "usertrees"|| $specify_suptreerecon eq "alltrees" || $specify_suptreerecon eq "yaptp") equal comparisons taxa quartets splits comparisons Sorry, the quartets, taxa, and splits weight option cannot be used with the dfit criterion perl ($specify_weighttype eq "quartets" || $specify_weighttype eq "splits" || $specify_weighttype eq "taxa") && $specify_criterion eq "dfit" Sorry, the splits and comparison weight options cannot be used with the qfit criterion perl ($specify_weighttype eq "splits" || $specify_weighttype eq "comparisons") && $specify_criterion eq "qfit" Sorry, the comparisons, taxa, and quartets weight options cannot be used with the sfit criterion perl ($specify_weighttype eq "quartets" || $specify_weighttype eq "taxa" || $specify_weighttype eq "comparisons") && $specify_criterion eq "sfit" Please specify the weight used to normalise the scoring system perl $specify_suptreerecon ne "nj" && $specify_suptreerecon ne "consensus" && !defined $specify_weighttype This option specifies the weight used to normalise the scoring system for large (or small) tree bias. Depending on the optimality criteria used (see set command) there are different weighting schemes. Using the dfit optimality criterion, the options are: equal or comparisons. equal applies no normalisation and comparisons normalises so every tree has the same vote (regardless of tree size). - Using the qfit optimality criterion, the options are: equal or taxa or quartets. equal applies no normalisation; taxa applies a normalisation that is calculated as n-3. quartets normalises so every tree has the same vote (regardless of tree size). Using the sfit optimality criterion, the options are: equal or splits; equal applies no normalisation. splits normalises so every tree has the same vote (regardless of tree size). specify_consensus Consensus method (Consensus and Bootstrap) perl ($specify_suptreerecon eq "consensus" || $specify_suptreerecon eq "bootstrap") strict majrule minor user Please specify a consensus method perl ($specify_suptreerecon eq "consensus" || $specify_suptreerecon eq "bootstrap") && !defined $specify_consensus This specifies the method to use to for consensus trees Strict specifies that the consensus should only include relationships that appear 100% of the time in the bootstrapped trees. Majority Rule specifies that the consensus should only include relationships that appear great than 50% of the time in the bootstrapped trees. Minor specifies that that the consensus should only include relationships that appear great than 50% of the time in the universally distributed trees, but that the minor components that are compatible with the majority-rule tree should also be included. User can specify a proportion (greater than 0.5 and lessthan 1.0) that should be the minimum proportion that any relationship should appear in the universally specify_consensusfr Consensus fraction perl $specify_consensus eq "user" 0.50 The value for the consensus proportion must be between 0.5 and 1 perl ($specify_consensusfr < 0.5 || $specify_consensusfr > 1) Please enter a value for the consensus proportion between 0.5 and 1 perl !defined $specify_consensusfr && $specify_consensus eq "user" specify_method Method to randomize input trees (YAPTP only) perl $specify_suptreerecon eq "yaptp" equiprobable markovian equiprobable Please specify a randomization method perl $specify_suptreerecon eq "yaptp" && !defined $specify_method This option sets the method to be used to construct the random supertrees. The most desirable method is equiprobable as this gives any tree in supertree space an equal chance of being chosen. This however is not always possible to use as it requires the knowledge of how many supertrees there are in supertree space. This becomes difficult to calculate when the number of taxa becomes large. By default the generatetrees command will use the equiprobable method. specify_printscores Print source scores (usertrees/avcon only) perl $specify_suptreerecon eq "usertrees" yes no no Please specify whether or not to print source scores perl $specify_suptreerecon eq "usertrees" && !defined $specify_printscores specify_create Create a file containing all trees (alltrees only) perl $specify_suptreerecon eq "alltrees" yes no no Please specify whether to create a file with all trees perl !defined $specify_create This option will write all the trees in supertree space along with their scores to the file alltrees.txt. This command should be used with caution, as with large numbers of taxa, the resulting file can be very large. specify_range Specify a range of trees number1 - number2 or all (alltrees only) perl $specify_suptreerecon eq "alltrees" This command specifies a range of trees for the alltrees method. Search treespace in the area between tree number x and y. For example if there were 10 taxa in the supertree then supertree space would contain 2,027,025 trees. This could take a prohibitively long time on a single computer, but this option allows the user to get different computers to search different parts of tree space. i.e. "range 1-1000000"" or "range 1000001-2027025" specify_parsornj Method to use for MRP (analysis; MRP only) perl $specify_criterion eq "mrp" parsimony nj parsimony Please set the analysis method for MRP to parsimony or neighbor joining perl !defined $specify_parsornj && $specify_criterion eq "mrp" This specifies the method to use to estimate the missing data in the average consensus analysis. By default this is set to 4point which is the 4-point condition estimate specify_usertrees Select your Usertrees file perl $specify_suptreerecon eq "usertrees" usertrees.txt Please specify a file with your usertrees to evaluate perl !defined $specify_usertrees && $specify_suptreerecon eq "usertrees" Provide the tree files to analyze in phylip format specify_missingdata Method to handle missing data (missing; nj only) perl $specify_suptreerecon eq "nj" 4point ultrametric 4point Please enter a method to handle missing data perl !defined $specify_missingdata && $specify_suptreerecon eq "nj" This specifies the method to use to estimate the missing data in the average consensus analysis. By default this is set to 4point which is the 4-point condition estimate consensus_guidetree Select a guidetree for Consensus perl $specify_suptreerecon eq "consensus" guidetree.tre all-outfiles *