MultAlin creates a multiple sequence alignment from a group of related sequences using progressive pairwise alignments.

References:

• Corpet, F. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Research, 1988 Nov;16(22):10881–10890.

• MultAlin Server
• Documentation (Also in $MULTALIN_HOME/multalin.txt)

• Module Name: multalin (see the modules page for more information)
• Environment variables set
  • MULTALIN_HOME
• Example files in $MULTALIN_HOME/example

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load multalin

[user@cn3144 ~]$ ln -s $MULTALIN_HOME/example/cytc . 
[user@cn3144 ~]$ multalin cytc
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading cytc
Sequence #       0   1   2   3   4   5
Reading blosum62.tab
Saving Configuration.
Clustering with fast
CCPC50 with CCRF2S 
                                                                               
with CCRF2C 
                                                                               
with CCQF2R 
                                                                               
with CCQF2P 
                                                                               
CCRF2S with CCRF2C 
                                                                               
with CCQF2R 
                                                                               
with CCQF2P 
                                                                               
CCRF2C with CCQF2R 
                                                                               
with CCQF2P 
                                                                               
CCQF2R with CCQF2P 
                                                                               
Action successful 
Saving cytc.clu
Aligning
CCPC50 with CCRF2C Position #       129  101    1
                                                                               
CCQF2R with CCQF2P Position #       112  101    1
                                                                               
CCPC50 .with CCRF2S Position #       129  101    1
                                                                               
CCPC50 ..with CCQF2R .Position #       133  101    1
                                                                               
Action successful  1 iteration(s)
Saving cytc.cl2
Saving cytc.msf
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. multalin.sh). For example:

#!/bin/bash
set -e
module load multalin
ln -s $MULTALIN_HOME/example/cytc
multalin cytc

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] multalin.sh

Create a swarmfile (e.g. multalin.swarm). For example:

multalin input1
multalin input2
multalin input3

Submit this job using the swarm command.

swarm -f multalin.swarm [-g #] [-t #] --module multalin