MAFFT-Teaching

Category

Bioinformatics

Program On

Teaching

Version

7.313

Author / Distributor

MAFFT

Description

"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 <∼10,000 sequences), etc." More details are at MAFFT

Running Program

The last version of this application is at /usr/local/apps/eb/MAFFT/7.313-foss-2016b-with-extensions

To use this version, please load the module with

ml MAFFT/7.313-foss-2016b-with-extensions 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_MAFFT
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=MAFFT.%j.out
#SBATCH --error=MAFFT.%j.err

cd $SLURM_SUBMIT_DIR
ml MAFFT/7.313-foss-2016b-with-extensions
mafft [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml MAFFT/7.313-foss-2016b-with-extensions 
mafft -h

/usr/local/apps/eb/MAFFT/7.313-foss-2016b-with-extensions/bin/mafft: Cannot open -h.

------------------------------------------------------------------------------
  MAFFT v7.313 (2017/Nov/15)
  http://mafft.cbrc.jp/alignment/software/
  MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
------------------------------------------------------------------------------
High speed:
  % mafft in > out
  % mafft --retree 1 in > out (fast)

High accuracy (for <~200 sequences x <~2,000 aa/nt):
  % mafft --maxiterate 1000 --localpair  in > out (% linsi in > out is also ok)
  % mafft --maxiterate 1000 --genafpair  in > out (% einsi in > out)
  % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)

If unsure which option to use:
  % mafft --auto in > out

--op # :         Gap opening penalty, default: 1.53
--ep # :         Offset (works like gap extension penalty), default: 0.0
--maxiterate # : Maximum number of iterative refinement, default: 0
--clustalout :   Output: clustal format, default: fasta
--reorder :      Outorder: aligned, default: input order
--quiet :        Do not report progress
--thread # :     Number of threads (if unsure, --thread -1)

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Installation

Source code is obtained from MAFFT

System

64-bit Linux