How to use the clustal omega command line tool with custom gap penalty?

Question

[sodiumnitrate]

Hi all,

I compiled clustal omega (1.2.4) on my laptop and I can use it to align sequences by doing:

clustalo -i sequences.fasta -o output.fasta

in the terminal. I have checked both the help and the readme, but I can't find how to change the parameters for alignment, like the gap penalty, etc. There are online servers that let you do this (https://www.genome.jp/tools-bin/clustalw) or screenshots of GUI that allow for it, but how do I do this with the command line tool? What am I missing?

Answer 1

[GenoMax]

clustal omega and clustalw are two different programs.

From clustalo help:

Clustal Omega uses the HHalign algorithm and its default settings as its core alignment engine. The algorithm is described in Söding, J. (2005) 'Protein homology detection by HMM–HMM comparison'. Bioinformatics 21, 951-960.

The default transition matrix is Gonnet, gap opening penalty is 6 bits, gap extension is 1 bit.

Looks like you can't change these at run time.