MAFFT-Teaching
Category
Bioinformatics
Program On
Teaching
Version
7.273
Author / Distributor
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 <â¼200 sequences), FFT-NS-2 (fast; for alignment of <â¼10,000 sequences), etc." More details are at MAFFT
Running Program
The last version of this application is at /usr/local/apps/eb/MAFFT/7.273-foss-2016b-with-extensions
To use this version, please load the module with
ml MAFFT/7.273-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/7.273-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/7.273-foss-2016b-with-extensions mafft -h /usr/local/apps/eb/MAFFT/7.273-foss-2016b-with-extensions/bin/mafft: Cannot open -h. ------------------------------------------------------------------------------ MAFFT v7.273 (2016/2/20) 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)
Installation
Source code is obtained from MAFFT
System
64-bit Linux