Convert maf (multiple alignment file) to FASTA

[Avro1986]

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!

[themerlin]

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

[GenoMax]

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).

[JackieBadger]

Mira assembler has a small package to convert MAF to many formats

[themerlin]

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.