bp_run_protdist.pl man page on Fedora

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BP_RUN_PROTDIST(1)    User Contributed Perl Documentation   BP_RUN_PROTDIST(1)

NAME
       run_neighbor - run Phylip's 'protdist' program through Bioperl

SYNOPSIS
       run_protdist [-i inputfile] [-o outfilename]

DESCRIPTION
       Provide an alignment file to run protdist on.  File should be named
       either .aln or .phy.  This is required so that we can determine if we
       need to convert a clustalw alignment into phylip.  You are welcome to
       extend the script to work on other MSA formats which bioperl supports.
       This is intended to be used in very simple manual pipelines.

       The input file should be named in the form of file.phy or file.aln the
       program expects a file in the form of (\S+)\.(\S+).

       This will run the application 'protdist' using the 'KIMURA' formula to
       build a a protein distance matrix.  Those with phylip3.6 will want to
       make some changes if they want to use JTT.  I'm happy to help add this
       in as a cmd-line argument if it is requested.

AUTHOR
       Jason Stajich, jason-AT-open-bio-DOT-org

perl v5.14.1			  2011-07-21		    BP_RUN_PROTDIST(1)
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