Question: How to convert .XFMA file to .nexus file
0
gravatar for jeccy.J
4.6 years ago by
jeccy.J50
Argentina
jeccy.J50 wrote:

Hi Everyone.

I have generated an .xfam alignment file using Parsnp (harvest suit)

For phylogenetical analysis, I want to  usie BEAST program which requires the input file to be in NEXUS format.

I use bioperl  but somehow its not converting properly which need input for BEAUti.

use Bio::AlignIO;
 
$in  = Bio::AlignIO->new(-file => "parsnp.xmfa" ,
                         -format => 'xmfa');
$out = Bio::AlignIO->new(-file => ">parsnp_alignment.nexus",
                         -format => 'nexus');
 
while ( my $aln = $in->next_aln ) {
  $out->write_aln($aln);
}

Can anyone please help me out.

.nexus .xfma • 1.6k views
ADD COMMENTlink modified 2.2 years ago by hallishtw10 • written 4.6 years ago by jeccy.J50

Did you figure out how to do it? I am the same spot.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by hallishtw10
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