PAUPRat Not specified Parsimony ratchet searches using PAUP* Derek Sikes and Paul O. Lewis; David Swofford is the author of PAUP; Kevin Nixon is author of the Ratchet Sikes, D., and Lewis, P.O., "PAUPRat: A tool to implement Parsimony and Likelihood Ratchet searches using PAUP*" http://users.iab.uaf.edu/~derek_sikes/software2.htm 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 pauprat scheduler_input scheduler.conf perl "ChargeFactor=1.0\\n" . "nodes=1\\n" . "mem=2G\\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 - 168.0 perl $runtime < 0.1 || $runtime > 168.0 Please set a value for the runtime perl !defined $runtime perl "runhours=$value\\n" zipfilename 1 scheduler.conf perl "zipfilename=$value\\n" intiation_string perl "pauprat_expanse" 0 intiation_string2 perl "/expanse/projects/ngbt/opt/expanse/pauprat/march2000/pauprat setup.nex && paup4a168_expanse -n < paup_commands.txt" 0 infile Input Data (nexus format) infile.nex 0 paup_file paup_commands.txt 0 perl parameter_file1 setup.nex 1 perl parameter_file1 setup.nex 2 perl specify_nchar How many characters in your matrix? setup.nex 3 perl Please enter the number of characters in your matrix perl !defined $specify_nchar ratchet_params Ratchet Parameters specify_nreps How many ratchet reps should be run? setup.nex 4 perl 200 Please enter the number of ratchet reps perl !defined $specify_nreps specify_seed Set seed value setup.nex 5 perl 0 Please enter a seed value perl !defined $specify_seed If the seed value is set to 0, it tells PAUPRat to generate a random number seed for you. Otherwise, you may set to your preferred random number seed. The seed you choose determines the sequence of random numbers used in choosing characters to perturb for each iteration running PAUPRat twice with the same random number seed (other than 0) will result in exactly the same characters being perturbed each iteration the safest thing to do is let PAUPRat choose a new seed each time you run it. specify_pct setup.nex Specify the percentage of characters to perturb (-pct) 6 perl !defined $specify_mod perl 20 Sorry, you cannot specify both a fixed number (-nmod) and a percentage (-pct) of characters to modify perl defined $specify_pct && defined $specify_mod Please specify either a fixed number (-nmod) or a percentage (-pct) of characters to modify perl !defined $specify_pct && !defined $specify_mod PAUPrat can perturb either a percentage of the informative characters, or a specified number of the paramters. These are mutually exclusive parameters. Use -pct to specify a percentage of characters to perturb each iteration; use nmod to specify absolute number of characters to perturb each iteration; you cannot use both nmod and pct simultaneously. Nixon (1999b) states that perturbing between 5% and 25% of the total number of informative characters usually works well. specify_mod Specify the absolute number of characters to perturb (-nmod) setup.nex 7 perl Sorry, you cannot specify both a fixed number (-nmod) and a percentage (-pct) of characters to modify perl defined $specify_pct && defined $specify_mod PAUPrat can perturb either a percentage of the informative characters, or a specified number of the paramters. These are mutually exclusive parameters. Use -pct to specify a percentage of characters to perturb each iteration; use nmod to specify absolute number of characters to perturb each iteration; you cannot use both nmod and pct simultaneously. Nixon (1999b) states that perturbing between 5% and 25% of the total number of informative characters usually works well. specify_wtmode Set the weighting mode (-wtmode) setup.nex 8 perl uniform add mult uniform Set weigthing mode to uniform to ensure that original weights are always 1 for all characters. Set weighting mode to additive to handle the case of unequal original weights in an additive way. Additive means a character originally weighted 10 will act just like 10 separate characters each weighted 1: it will be 10 times more likely to be chosen for perturbation than a character whose original weight was 1, but each time it is chosen, its weight will be incremented by just 1. Set weighting mode to multiplicative to handle the case of unequal original weights in a multiplicative way. If multiplicative mode is chosen, a character originally weighted 10 will increase its weight by 10 each time it is selected for perturbation, but it will not be any more likely to be chosen than a character whose original weight was 1. specify_verbose Verbose or Terse output? setup.nex 9 verbose terse perl terse Specify verbose if you want comments in the output indicating which characters were perturbed and how much their weights changed for each iteration. Normally, you want to specify terse because these comments add a lot of bytes to the file and don't change the analysis at all setup_hidden setup.nex 10 perl setup_increase Increase setup.nex 11 perl auto no auto setup_hidden1 setup.nex 12 perl setup_hidden2 setup.nex 14 perl setup_hidden3 setup.nex 15 perl paup_params Paup Parameters setup_hidden4 Treat multistate taxa as uncertain setup.nex 16 1 setup_hidden4b setup.nex 16 perl $setup_hidden4 perl setup_hidden5 setup.nex 17 perl paup_branchalg Branch Swapping Algorithm (swap) setup.nex 19 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_rearrlimit Specify a rearrangement limit The search will be limited to the specified number of tree rearrangements (branch swaps). set_rearrlimitb setup.nex perl defined $set_rearrlimit 21 perl set_timelimit Specify a time limit (in seconds) The search will be limited to the specified number of tree rearrangements (branch swaps). set_timelimitb setup.nex perl defined $set_timelimit 22 perl set_reconlimit Specify a reconnection limit for PAUP The reconnection limit option limits the scope of SPR and TBR rearrangements. If an integer-value is specified, the value corresponds to the sum of the number of nodes between each reconnected branch and the nodes incident to the branch that was cut for pruning (SPR) or bisection (TBR). A rearrangement limit of 1 corresponds to nearest-neighbor interchanges. No entry sets the value to infinity. set_reconlimitb setup.nex perl defined $set_reconlimit 23 perl end_limits setup.nex 24 perl set_maxtrees Maximum number of trees saved (maxtrees) setup.nex 25 perl $set_multrees eq "yes" perl set_autoincrease Automatically increase the number of trees in memory setup.nex 26 perl $set_multrees eq "yes" perl auto no no set_increaseval Auto-increase amount (AutoInc). setup.nex 27 perl $set_autoincrease eq "auto" perl set_outgroup Specify an Outgroup 0 set_outgroupb Enter Your Outgroup Here setup.nex perl $set_outgroup 28 perl setup_hidden6 setup.nex 28 perl setup_hidden7 setup.nex 29 perl setup_hidden8 setup.nex 30 perl setup_hidden9 setup.nex 31 perl setup_hidden11 setup.nex 32 perl setup_hidden12 setup.nex 33 perl setup_hidden13 setup.nex 34 perl setup_hidden14 setup.nex 35 perl setup_hidden15 setup.nex 36 perl setup_hidden16 setup.nex 37 perl setup_hidden17 setup.nex 38 perl setup_hidden18 setup.nex 39 perl setup_hidden19 setup.nex 40 perl result_file paupratchet.log best_tree_file pauprat.best.tre tree_files mydata.tre run_data *.txt run_logs *.nex all_commandline COMMANDLINE