Converting .maf to FASTA for RAxML

[Christie Klinger]

Hello,

I have aligned a subset of bacterial genomes using Mugsy, which outputs an .maf file. I have since converted the .maf file to FASTA format. Currently, the FASTA file is in a multiple block format (multiple blocks of sequence per strain)-- should this FASTA file be converted to a single block of concatenated sequence per strain in order to run RAxML? Trying to find a good tool that might do this.

Thanks and please let me know if I need to clarify any other details,
-Christie K

[Andre J. Aberer]

Hi Christie,

I'd expect it to work.

In case, it does not work, maybe convert it to a .phy (Phylip)
file. Seaview is very straight-forward for this task and the output will
work definitely.

--
HTH,
Andre

--
Best regards,
Andre Aberer

PreDoc (Bioinformatics) in the Exelixis Lab, Heidelberg Institute for Theoretical Studies

[Christie Klinger]

Hi Andre,

Thanks for the quick reply!

When I leave the FASTA file formatted as multiple blocks per stain (more like the original .maf file), I get this error:

Fasta parsing error, RAxML expects an alignment.
the sequence before taxon >Rht_14_Assembly
: seems to have a different length

Concatenating all the blocks of sequence for each individual strain (20 total strains) fixes the problem.

Thanks for the Seaview tip-- it will be super helpful in the near future.

Regards,
-Christie

[Hiren Ghosh]

Do i need to concatenate using Seaview or else i upload the file and then save as in new name??

[Alexandros Stamatakis]

I am not sure I understand your question.

Alexis

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Research Group Leader, Heidelberg Institute for Theoretical Studies
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[Matthieu Muffato]

If you have BioPerl, this should work

-----------------
use Bio::AlignIO;

$in = Bio::AlignIO->new(-file => "inputfilename" ,
-format => 'maf');
$out = Bio::AlignIO->new(-file => ">outputfilename",
-format => 'phylip');

while ( my $aln = $in->next_aln ) {
$out->write_aln($aln);
}
-----------------

(taken from http://www.bioperl.org/wiki/HOWTO:AlignIO_and_SimpleAlign )

Matthieu