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Old 12-17-2012, 08:38 AM   #1
Avro1986
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Default 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!
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Old 12-17-2012, 09:09 AM   #2
themerlin
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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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Old 12-17-2012, 09:18 AM   #3
GenoMax
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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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Old 12-17-2012, 10:54 AM   #4
JackieBadger
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Mira assembler has a small package to convert MAF to many formats
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Old 12-17-2012, 11:12 AM   #5
themerlin
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Quote:
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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