How to cluster sequences using HMMER?

[Loczi94]

Hi everyone!

I have a fasta file with transposons sequences and I have to cluster them using HMMER. Does anyone know how I can do it? I browsed HMMER's documentation but it didn't help..

I hope that someone would be able to help me. Thanks in advance.

[GenoMax]

If you just want to cluster the sequences then CD-HIT would be simpler to use.

[Loczi94]

I clustered the sequences with BlastClust, but now I have to do it using HMMER (it's a part of my project).

[GenoMax]

Are you referring to building a profile HMM rather than a cluster then?

[Loczi94]

No, I'm supposed to group the sequences into clusters. I don't think I need HMM profiles. (Maybe in some latter phases of the project.)