POY
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
infile_ - Primary Input File
infile2_ - InFile - Input File
infile3_ - InFile - Input File
infile4_ - InFile - Input File
infile5_ - InFile - Input File
infile6_ - InFile - Input File
substitutions_ - Integer - Substitution cost
indels_ - Integer - Individual insertion and deletion cost
gapopening_ - Integer - Gap opening cost
terminalsfile_ - InFile - Terminals file
synonyms_ - InFile - Synonyms file
outgroup_ - String - Outgroup
constraint_ - InFile - Constraint tree
randomseed_ - Integer - Random seed for the program initialization.
Section: ****************************************************************************
supportparagraph
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support_ - Excl - Support calculation (requires a tree in one of the
input files)
pseudoreplicates_ - Integer - Number of pseudoreplicates for bootstrap and jakknife
remove_ - Integer -
Percentage of characters to be removed per
pseudoreplicate during jackknife
outputfile_ - Results -