MAFFT

Description

MAFFT is a fast multiple sequence alignment program for aminoacids and nucleotids. According to number of sequences and demands to time and accuracy it offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.

License

Free for academic users

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of mafft and load default version of mafft as

module avail mafft/ # list available modules
module load mafft   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail mafft

and choose explicit version you want to use.

mafft [arguments] input > output

Documentation

http://mafft.cbrc.jp/alignment/software/manual/manual.html

Homepage

http://mafft.cbrc.jp/alignment/software/
http://mafft.cbrc.jp/alignment/software/source.html