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  • Loczi94
    Junior Member
    • Mar 2016
    • 6
    #1

    How to cluster sequences using HMMER?

    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.
    Tags: cluster hmmer
  • GenoMax
    Senior Member
    • Feb 2008
    • 7142
    #2
    If you just want to cluster the sequences then CD-HIT would be simpler to use.

    Comment

    • Loczi94
      Junior Member
      • Mar 2016
      • 6
      #3
      I clustered the sequences with BlastClust, but now I have to do it using HMMER (it's a part of my project).

      Comment

      • GenoMax
        Senior Member
        • Feb 2008
        • 7142
        #4
        Are you referring to building a profile HMM rather than a cluster then?

        Comment

        • Loczi94
          Junior Member
          • Mar 2016
          • 6
          #5
          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.)

          Comment

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