Kalign is a fast multiple sequence alignment program for biological sequences.

References:

• Timo Lassmann. Kalign 3: multiple sequence alignment of large data sets. Bioinformatics (2020).
• Timo Lassmann, Oliver Frings, and Erik LL Sonnhammer. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic acids research 37.3 (2008): 858-865.
• Timo Lassmann and Erik LL Sonnhammer. Kalign: an accurate and fast multiple sequence alignment algorithm.
BMC bioinformatics 6.1 (2005): 298.

• kalign Main Site

• Module Name: kalign (see the modules page for more information)
• Multithreaded via the -n/--nthreads argument.
• Environment variables set
  • KALIGN_HOME
• Example files in $KALIGN_HOME/test

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 kalign

[user@cn3144 ~]$ kalign -f fasta -i $KALIGN_HOME/test/small.fa -o out.afa

Kalign (3.4.0)

Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann

This program comes with ABSOLUTELY NO WARRANTY; for details type:
`kalign -showw'.
This is free software, and you are welcome to redistribute it
under certain conditions; consult the COPYING file for details.

Please cite:
  Lassmann, Timo.
  "Kalign 3: multiple sequence alignment of large data sets."
  Bioinformatics (2019)
  https://doi.org/10.1093/bioinformatics/btz795

[2024-08-23 17:47:26] :     LOG : Detected DNA sequences.
[2024-08-23 17:47:26] :     LOG : Read 17 sequences from /usr/local/apps/kalign/3.4.0/test/small.fa.
[2024-08-23 17:47:26] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-08-23 17:47:26] :     LOG : Calculating pairwise distances
[2024-08-23 17:47:26] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-08-23 17:47:26] :     LOG : Building guide tree.
[2024-08-23 17:47:26] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-08-23 17:47:26] :     LOG : Aligning
[2024-08-23 17:47:26] :     LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load kalign
kalign -f fasta -i $KALIGN_HOME/test/small.fa -o out.afa

Submit this job using the Slurm sbatch command.

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

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

kalign -f fasta -i set1.fa -o set1.afa
kalign -f fasta -i set2.fa -o set2.afa
kalign -f fasta -i set3.fa -o set3.afa
kalign -f fasta -i set4.fa -o set4.afa

Submit this job using the swarm command.

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