main ()
%(filename)s
Creates an execution script for various analysis using PAUP.
Nucleotide sequences are supplied either as one or more fasta format
files or in a single nexus format file.
{{nex nexus file}}
{{m method
nj nj tree
jack jackknife analysis using nj
boot bootstrap analysis using nj
dist write square distance matrix
tstv estimate transition/transversion ratio}}
{{e execute paup on output file}}
{{nocod a list of codons to exclude, eg 5-8,12}}
{{h Prints documentation.}}
{{v verbosity
1}}
{{out name of outfile
stdout}}
{{version print version info and exit}}
%(version)s
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