Any script or program to change aln file into fasta?
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2.8 years ago
MichaelTrev ▴ 10

Hello! I have a problem with format files. I need to compare the score from two alignments. One is in ".afa" format, second has ".aln" format (after t-coffee alignment). I have to use a mscore tool, but in command it requires two fasta files. ".afa" is ok, but how can i convert ".aln" to fasta?

Now I do it in http://www.sing-group.org/ALTER/. But here I can only convert one file at a time. I need to convert several hundred files.

Any advice?

fasta aln format • 2.6k views
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2.8 years ago

There's the perl fasconvert utility in the FAST module or the seqret utility from EMBOSS.

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Thank u for an answer. I just downloaded and build emboss on my PC, can u give me an example of how to use it properly? I have file "a.aln" and I need it in ".fasta". I'm tried to read doc's but can't find it.

EDIT: Ok i got it ! It's just "seqret" command ! Thank u so much for help!

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