1BP_SEARCH2TRIBE(1)    User Contributed Perl Documentation   BP_SEARCH2TRIBE(1)
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NAME

6       search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
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SYNOPSIS

9       Usage:
10         search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1
11       file2 ..
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DESCRIPTION

14       This script is probably too slow for most people's uses.  It is better
15       to use something like scripts/searchio/fastam9_to_table, -m 9 output
16       from BLAST, or the blast2table from the BLAST O'Reilly book to get a
17       tabular output from these programs and then feed the table into MCL
18       with the mcxdeblast script and the --m9 option.
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20       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH)
21       into a Markov Matrix for TribeMCL clustering.
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23       The options are:
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25          -o filename          - the output filename [default STDOUT]
26          -f format            - search result format (blast, fasta)
27                                 (ssearch is fasta format). default is blast.
28          -w or --weight VALUE - Change the default weight for E(0.0) hits
29                                 to VALUE (default=200 (i.e. 1e-200) )
30          -h                   - this help menu
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32       Additionally specify the filenames you want to process on the command-
33       line.  If no files are specified then STDIN input is assumed.  You
34       specify this by doing: search2tribe < file1 file2 file3
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AUTHOR

37       Jason Stajich, jason-at-bioperl-dot-org
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41perl v5.12.0                      2010-04-29                BP_SEARCH2TRIBE(1)