4.a168 Phylogenetic Analyses Using Parsimony* David Swofford 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_expanse_xsede initiation_string perl "paup4a168_expanse -n < paup_commands.txt" 0 infile Input Data (nexus format) infile.nex 0 paup_commandsa1 paup_commands.txt 1 perl $optimality_specified ne "Parsimony" perl paup_commandsa2 paup_commands.txt 1 perl $optimality_specified eq "Parsimony" perl paup_commandsc paup_commands.txt 2 perl paup_scheduler scheduler.conf perl $optimality_specified ne "Parsimony" perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=4G\\n" . "cpus-per-task=2\\n" . "threads_per_process=2\\n" paup_scheduler_likelihood scheduler.conf perl $optimality_specified eq "Parsimony" && !$more_memory perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=2G\\n" . "cpus-per-task=1\\n" . "threads_per_process=1\\n" paup_scheduler_likelihood2 scheduler.conf perl $optimality_specified eq "Parsimony" && $more_memory perl "nodes=1\\n" . "node_exclusive=0\\n" . "mem=6G\\n" . "cpus-per-task=1\\n" . "threads_per_process=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" The job will run on 2 processors as configured. If it runs for the entire configured time, it will consume 2 x $runtime cpu hours perl $optimality_specified ne "Parsimony" The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume 1 x $runtime cpu hours perl $optimality_specified eq "Parsimony" Estimate the maximum time your job will need to run. We recommend testing initially with a time less than 0.5hr test run because Jobs set for 0.5 h or less depedendably run immediately in the "debug" queue. Once you are sure the configuration is correct, you then increase the time. This is because queue waits can be longer for jobs configured for the full 168 hours. paupblock 1 My data set has commands in a PAUP block 1 This interface requires a PAUP block in the input file. perl !$paupblock optimality_specified Set the Optimality Criterion Parsimony Parsimony Parsimony Likelihood Likelihood Distance Distance more_memory My Parsimony run requires more memory perl $optimality_specified eq "Parsimony" 0 result_files *