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  • kajsa
    Member
    • Jan 2010
    • 19
    #1

    What is the best program for MSA of 33 very similar sequences 113 00 bp long?

    Hello,

    I want to do a multiple sequence alignment with 33 sequences that are 99,99% similar and are around 113000 bp long.

    I have looked around and found MAFFT and MAUVE. Are there any other programs to use that I've missed?

    Thankful for any advise.
    Kajsa
    Tags: None
    • colindaven
      Senior Member
      • Oct 2008
      • 417
      #2
      Muscle might be good. MUGSY is probably excellent for this use case given the length of the sequence.

      cheers
      Colin

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        • kajsa
          Member
          • Jan 2010
          • 19
          #3
          Originally posted by colindaven View Post
          Muscle might be good. MUGSY is probably excellent for this use case given the length of the sequence.

          cheers
          Colin
          Thanks a lot!
          Kajsa

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