ILRI Research Computing

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====== mafft ======
MAFFT is a multiple sequence alignment program for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc. 

  * Latest Version: 7.475
  * Added: October, 2011
  * Updated: September, 2023
  * Link: https://mafft.cbrc.jp/alignment/software

===== Usage =====
Show all available versions:

<code>$ module avail mafft</code>

Load one version into your environment and run it:

<code>$ module load mafft/7.505
$ mafft</code>

===== Installation =====
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://mafft.cbrc.jp/alignment/software/mafft-7.505-with-extensions-src.tgz
$ tar xf mafft-7.505-with-extensions-src.tgz 
$ cd mafft-7.505-with-extensions/core
$ sed -i 's/PREFIX = \/usr\/local/PREFIX = \/export\/apps\/mafft\/7.505/' Makefile
$ make
$ sudo mkdir -p /export/apps/mafft/7.505
$ sudo chown aorth /export/apps/mafft/7.505
$ make install
$ cd ../extensions
$ vim Makefile
$ sed -i 's/PREFIX = \/usr\/local/PREFIX = \/export\/apps\/mafft\/7.505/' Makefile
$ make
$ make install
$ sudo chown -R root:root /export/apps/mafft/7.505</code>