Codon Alignment

Standalone version of Codon Alignment from Los Alamos National Laboratory.

Description

The staff at LANL kindly provided me with the standalone version of their tool for translation aware alignment. The original tool is written in perl and is able to read sequences in (almost?) any format. I packaged a minimal standalone version that works only with fasta files by writing a wrapper in python for the core program codonalign.

Usage

It needs python (2.7) and perl. Only Biopython is needed as external dependency (though it would be easy to do without). Running ca_wrapper -h gives the usual help

[user@host CodonAlign]$ ca_wrapper.py -h
usage: ca_wrapper.py [-h] [-f FILENAME] [-r FRAME] [-s FS_COMP]

Run codon align as in
http://www.hiv.lanl.gov/content/sequence/CodonAlign/codonalign.html

optional arguments:
  -h, --help            show this help message and exit
  -f FILENAME, --file FILENAME
                        input file in fasta format <sample.fasta>
  -r FRAME, --frame FRAME
                        frame [1, 2 or 3], otherwise best is determined
  -s FS_COMP, --fs_comp FS_COMP
                        max n of compensating frameshifts <5>

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Licensing

Code is released under the GNU GPL version 2.0. For the script codonalign, obtained from LANL, please consider the following statement as well.

The script has been approved by LANL/LANS for open source release.
Include the following copyright and disclaimer. [JM 2012]

Copyright 2012.  Los Alamos National Security, LLC. This material was produced under
U.S. Government contract DE-AC52-06NA25396 for Los Alamos National Laboratory (LANL),
which is operated by Los Alamos National Security, LLC for the U.S. Department of
Energy. The U.S. Government has rights to use, reproduce, and distribute this software.
NEITHER THE GOVERNMENT NOR LOS ALAMOS NATIONAL SECURITY, LLC MAKES ANY WARRANTY, EXPRESS
OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE.  If software is
modified to produce derivative works, such modified software should be clearly marked,
so as not to confuse it with the version available from LANL.

Additionally, this program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free Software
Foundation; version 2.0 of the License. Accordingly, this program is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
Public License for more details.