xenial (1) bp_run_protdist.pl.1p.gz

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