NAME

       bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

SYNOPSIS

       Usage:
         bp_search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..

DESCRIPTION

       This script is probably too slow for most people's uses.  It is better to use something like
       scripts/searchio/fastam9_to_table, -m 9 output from BLAST, or the blast2table from the BLAST O'Reilly
       book to get a tabular output from these programs and then feed the table into MCL with the mcxdeblast
       script and the --m9 option.

       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL
       clustering.

       The options are:

          -o filename          - the output filename [default STDOUT]
          -f format            - search result format (blast, fasta)
                                 (ssearch is fasta format). default is blast.
          -w or --weight VALUE - Change the default weight for E(0.0) hits
                                 to VALUE (default=200 (i.e. 1e-200) )
          -h                   - this help menu

       Additionally specify the filenames you want to process on the command-line.  If no files are specified
       then STDIN input is assumed.  You specify this by doing: bp_search2tribe < file1 file2 file3

AUTHOR

       Jason Stajich, jason-at-bioperl-dot-org