Clustal Omega
Clustal Omega is a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
To load this on Palmetto 2 please run the following:
module load biocontainers
module load clustalo
To execute an alignment clustal omega expects an input Fasta file that consists of all your sequences.
It is recommended that if you are aligning only two sequences to use other pair end alignment tools. Checkout our other options in the Alignment Tools Section in the sidebar menu!
An example alignment command would look roughly like:
clustalo -i INPUT.fasta -o OUTPUT.fasta --threads=7
This tool can utilize multiple threads to speed things up!
This tool will assume the output destination is standard out if no output file is provided in the command!
Parallel Capabilities : Multithreading options available.