paupboot.py

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             { [nj] | jack | boot | dist | tstv } 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             { [1] } verbosity
-out           { [stdout] } name of outfile
-version       print version info and exit

$Id: paupboot.py,v 1.1 2004/10/10 02:53:10 nghoffma Exp $