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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

    Comment

    • 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

      Comment

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