Sort protein sequences according to their sequence similarity

Question

[Josep Ollé]

Dear all,

PROBLEM: I am having some problems doing a phylogenetic analysis for a study. Basically, I have a pool of around 1200 protein sequences from hemagglutinin (influenza virus), and I would like to sort them according to their subtype group (so according to their sequence similarity), for further study their sequence differences within the groups. However, I do not find any software that is helping me with that, for now, I have tried MegaX, and is not helping.

QUESTION: Does anyone know of any software or method to do that? Any recommendations/suggestions are very much appreciated! :)

Thank you very much.

[cpad0112]

CD-HIT

Answer 1

[Mensur Dlakic]

It seems that you want to cluster sequences by similarity rather than sort them. I suggest MCL. There is an explanation and a number of scripts on the main web page if you are willing to read through it. Or you can search for MCL clustering and there will be lots of solutions out there.