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  • Avro1986
    Member
    • Dec 2012
    • 10
    #1

    Convert maf (multiple alignment file) to FASTA

    Hi everyone,

    I have aligned 9 genomes into a maf file. Now, I am trying to convert it into a FASTA file. Does anyone know how?

    Thank you!
    Tags: None
  • themerlin
    Member
    • Feb 2010
    • 51
    #2
    The galaxy tool is built on these libraries (https://bitbucket.org/james_taylor/bx-python/wiki/Home). They also include scripts to join blocks together before converting to fasta

    Comment

    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #3
      If you are familiar with galaxy (http://usegalaxy.org) then use the "Convert formats" --> "MAF to Fasta" implementation (actual libraries behind the GUI in "themerlin" post above).

      Comment

      • JackieBadger
        Senior Member
        • Mar 2009
        • 385
        #4
        Mira assembler has a small package to convert MAF to many formats

        Comment

        • themerlin
          Member
          • Feb 2010
          • 51
          #5
          Mira assembler has a small package to convert MAF to many formats
          Mira MAF is different than the MAF produced by whole genome aligners - the Mira MAF is unique to that program.

          Comment

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