PAUPRAT
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
specify_nchar_ - Integer - How many characters in your matrix?
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ratchet_params
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specify_nreps_ - Integer - How many ratchet reps should be run?
specify_seed_ - Integer - Set seed value
specify_pct_ - Integer - Specify the percentage of characters to perturb (-pct)
specify_mod_ - Integer - Specify the absolute number of characters to perturb (-nmod)
specify_wtmode_ - Excl - Set the weighting mode (-wtmode)
specify_verbose_ - Excl - Verbose or Terse output?
setup_increase_ - Excl - Increase
setup_nrep_ - Integer - How Many Reps (nrep=)
Section: ****************************************************************************
paup_params
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setup_hidden4_ - Switch - Treat multistate taxa as uncertain
paup_branchalg_ - Excl - Branch Swapping Algorithm (swap)
set_multrees_ - Excl - Save all optimal trees? (multrees)
set_rearrlimit_ - Integer - Specify a rearrangement limit
set_timelimit_ - Integer - Specify a time limit (in seconds)
set_reconlimit_ - Integer - Specify a reconnection limit for PAUP
set_maxtrees_ - Integer - Maximum number of trees saved (maxtrees)
set_autoincrease_ - Excl - Automatically increase the number of trees in memory
set_increaseval_ - Integer - Auto-increase amount (AutoInc).
set_outgroup_ - Switch - Specify an Outgroup
set_outgroupb_ - String - Enter Your Outgroup Here
result_file_ - Results -
best_tree_file_ - Results -
run_data_ - Results -
run_logs_ - Results -
all_commandline_ - Results -