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

6       run_neighbor - run Phylip's 'protdist' program through Bioperl
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SYNOPSIS

9       run_protdist [-i inputfile] [-o outfilename]
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DESCRIPTION

12       Provide an alignment file to run protdist on.  File should be named
13       either .aln or .phy.  This is required so that we can determine if we
14       need to convert a clustalw alignment into phylip.  You are welcome to
15       extend the script to work on other MSA formats which bioperl supports.
16       This is intended to be used in very simple manual pipelines.
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18       The input file should be named in the form of file.phy or file.aln the
19       program expects a file in the form of (\S+)\.(\S+).
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21       This will run the application 'protdist' using the 'KIMURA' formula to
22       build a a protein distance matrix.  Those with phylip3.6 will want to
23       make some changes if they want to use JTT.  I'm happy to help add this
24       in as a cmd-line argument if it is requested.
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AUTHOR

27       Jason Stajich, jason-AT-open-bio-DOT-org
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31perl v5.8.8                       2007-04-19                BP_RUN_PROTDIST(1)
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