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  • 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!

  • #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

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    • #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).

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      • #4
        Mira assembler has a small package to convert MAF to many formats

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        • #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.

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