clustal_omega.md

+++
title = "Clustal Omega"
description =  "How to run Clustal Omega on HCC resources"
weight = "10"
+++


[Clustal Omega](http://www.clustal.org/omega/) is a general purpose multiple sequence alignment (MSA) tool used mainly with protein, as well as DNA and RNA sequences. Clustal Omega is fast and scalable aligner that can align datasets of hundreds of thousands of sequences in reasonable time.


The general usage of Clustal Omega is:
{{< highlight bash >}}
$ clustalo -i input_file.fasta -o output_file.fasta [options]
{{< /highlight >}}
where **input_file.fasta** is the multiple sequence input file in `fasta` format, and **output_file.fasta** is the multiple sequence alignment output file in `fasta` format.


Clustal Omega accepts 3 types of sequence input files:

- sequence file with aligned/unaligned sequences
- multiple alignment in a file/profile of aligned sequences
- Hidden Markov Model (HMM) 

These input files must contain at least 2 sequences and must be in one of the following MSA file formats: `a2m`, `fa[sta]`, `clu[stal]`, `msf`, `phy[lip]`, `selex`, `st[ockholm]`, `vie[nna]`. Moreover, if not specified, the generated output file is in `fasta` format.


More Clustal Omega options can be found by typing:
{{< highlight bash >}}
$ clustalo -h
{{< /highlight >}}


Running Clustal Omega on Crane with input file `input_reads.fasta` with `8 threads` and `10GB memory` is shown below:
{{% panel header="`clustal_omega.submit`"%}}
{{< highlight bash >}}
#!/bin/bash
#SBATCH --job-name=Clustal_Omega
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=10:00:00
#SBATCH --mem=10gb
#SBATCH --output=ClustalOmega.%J.out
#SBATCH --error=ClustalOmega.%J.err

module load clustal-omega/1.2

clustalo -i input_reads.fasta -o output_msa.sto --outfmt=st 	--threads=$SLURM_NTASKS_PER_NODE
{{< /highlight >}}
{{% /panel %}}

The output file `output_msa.sto` contains the resulting multiple sequence alignments in Stockholm format (**--outfmt=st**).

Moreover, if you change the command above with:
{{< highlight bash >}}
$ clustalo -i input_reads.sto --dealign -v
{{< /highlight >}}
Clustal Omega will read the input file in Stockholm format, de-align the sequences, and then re-align them, printing progress report in meanwhile (**-v**). Because it is not specified, the output will be in the default `fasta` format.


### Clustal Omega Output

The basic Clustal Omega output produces one alignment file in the specified output format. More intermediate outputs can be generated using specific Clustal Omega options, such as: **--distmat-out=<file>** (*pairwise distance matrix output file*) and **--guidetree-out=<file>** (*guide tree output file*).


### Useful Information

In order to test the Clustal Omega performance, we used three DNA and protein input fasta files, `data_1.fasta`, `data_2.fasta`, `data_3.fasta`. Some statistics about the input files and the time and memory resources used by Clustal Omega are shown on the table below:
{{< readfile file="/static/html/clustal_omega.html" >}}