NAME

bp_mrtrans - implement a transformer of alignments from protein to mrna coordinates

SYNOPSIS

Usage: bp_mrtrans -i inputfile -o outputfile [-if input format] [-of output format] [-s cDNA sequence database] [-sf cDNA sequence format] [-h]

DESCRIPTION

This script will convert a protein alignment back into a cDNA. Loosely based on Bill Pearson's mrtrans.

The options are:

-o filename          - the output filename [default STDOUT]
-of format           - output sequence format
                       (multiple sequence alignment)
                       [default phylip]
-i filename          - the input filename [required]
-if format           - input sequence format
                       (multiple sequence alignment)
                       [ default clustalw]
-s --seqdb filename  - the cDNA sequence database file
-sf --seqformat      - the cDNA seq db format (flatfile sequence format)
-h                   - this help menu

AUTHOR

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