1BP_SEARCH2TRIBE(1)    User Contributed Perl Documentation   BP_SEARCH2TRIBE(1)
2
3
4

SYNOPSIS

6       Usage:
7         search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1
8       file2 ..
9

DESCRIPTION

11       This script is probably too slow for most people's uses.  It is better
12       to use something like scripts/searchio/fastam9_to_table, -m 9 output
13       from BLAST, or the blast2table from the BLAST O'Reilly book to get a
14       tabular output from these programs and then feed the table into MCL
15       with the mcxdeblast script and the --m9 option.
16
17       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH)
18       into a Markov Matrix for TribeMCL clustering.
19
20       The options are:
21
22          -o filename          - the output filename [default STDOUT]
23          -f format            - search result format (blast, fasta)
24                                 (ssearch is fasta format). default is blast.
25          -w or --weight VALUE - Change the default weight for E(0.0) hits
26                                 to VALUE (default=200 (i.e. 1e-200) )
27          -h                   - this help menu
28
29       Additionally specify the filenames you want to process on the com‐
30       mand-line.  If no files are specified then STDIN input is assumed.  You
31       specify this by doing: search2tribe < file1 file2 file3
32

AUTHOR

34       Jason Stajich, jason-at-bioperl-dot-org
35
36
37
38perl v5.8.8                       2007-05-07                BP_SEARCH2TRIBE(1)