# mafft.rb

Path: | lib/bio/appl/mafft.rb
Last Update: | Thu Nov 19 15:47:02 +0000 2009

# bio/appl/mafft.rb - MAFFT wrapper class

Copyright: | Copyright (C) 2003 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
License: | The Ruby License

     $Id: mafft.rb,v 1.18 2007/07/16 12:27:29 ngoto Exp $

Bio::MAFFT is a wrapper class to execute MAFFT. MAFFT is a very fast multiple sequence alignment software.

# Important Notes

Though Bio::MAFFT class currently supports only MAFFT version 3, you can use MAFFT version 5 because the class is a wrapper class.

## References

- K. Katoh, K. Misawa, K. Kuma and T. Miyata. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30: 3059-3066, 2002. nar.oupjournals.org/cgi/content/abstract/30/14/3059
- www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/

### Required files

tempfile bio/command bio/db/fasta bio/io/flatfile

[Validate]