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bp_search2tribep - Online in the Cloud

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This is the command bp_search2tribep that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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