PAUP 4.0b Phylogenetic Analyses Using Parsimony* David Swofford is the author of PAUP Swofford, D. L. 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts. Phylogeny / Alignment http://paup.csit.fsu.edu paup_2 initiation_string perl "/projects/ps-ngbt/opt/comet/paup/paup4a150/paup4a150_centos64 -n < paup_commands.txt" 0 infile Input Data (nexus format) infile.nex 0 paup_commandsb paup_commands.txt 1 perl !$paupblock perl paup_commandsa paup_commands.txt 0 perl paup_commandsc paup_commands.txt 2 perl raxmlhpc_hybridlogic2_scheduler scheduler.conf perl "threads_per_process=$nthreads_specified\\n" . "node_exclusive=0\\n" . "nodes=1\\n" runtime 1 scheduler.conf Maximum Hours to Run (click here for help setting this correctly) 0.5 Please set maximum hours to a value less than 168 h perl $runtime > 168.0 Please set maximum hours to run to a value greater than 0.1 h perl $runtime < 0.1 perl "runhours=$value\\n" Estimate the maximum time your job will need to run. We recommend testing 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. This is because queue waits can be longer for jobs configured for the full 168 hours. paupblock 1 scheduler.conf My data set has commands in a PAUP block 0 paup_params PAUP Parameters setup_header paup_block.nex 16 perl !$paupblock perl nthreads_specified How many threads? 1 Sorry you cant use more than 12 threads perl $value > 12 Please specify how many threads perl !$nthreads_specified setup4 Treat multistate taxa as uncertain paup_block.nex perl !$paupblock 16 1 setup4_hidden paup_block.nex 16 perl !$paupblock perl paup_branchalg Branch Swapping Algorithm (swap) paup_block.nex 19 perl !$paupblock tbr spr nni tbr PAUP uses three branch-swapping algorithms. In order of increasing effectiveness, these are (1) nearest neighbor interchanges (NNI, equivalent to the "local" procedure used in Versions 1 and 2 of PAUP); (2) subtree pruning-regrafting (SPR, approximately, but not exactly, equivalent to the "global" procedure used in earlier versions of PAUP); and (3) tree bisection-reconnection (TBR, a new procedure). set_multrees Save all optimal trees? (multrees) paup_block.nex 20 perl !$paupblock yes no no use multrees = no setup_hidden5 paup_block.nex 17 perl !$paupblock perl result_files *