[Bioperl-l] Nexus symbols
Luis M Rodriguez-R
me at miguel.weapps.com
Wed Sep 30 22:16:38 UTC 2009
Dear all,
Is there a way to remove the "symbols" (i.e. the 'symbols="ATCG"')
from the "format" line in the Nexus output of Bio::AlignIO?
My code (snippet) is:
my $fasta_i = Bio::AlignIO->new(-file=>"<$outfile.aln.fasta", '-
format'=>"fasta");
my $nexus_o = Bio::AlignIO->new(-file=>">$outfile.aln.nex", '-
format'=>"nexus");
while(my $fasta_aln=$fasta_i->next_aln){$nexus_o-
>write_aln($fasta_aln);}
And I would like to remove the symbols (is not compatible with MrBayes
v3.1.2: "Could not find parameter "symbols"").
Also, it would be nice to be able to change the TITLE comment.
Thanks all!
Regards,
Luis M. Rodriguez-R
[http://bioinf.uniandes.edu.co/~miguel/]
---------------------------------
Unidad de Bioinformática del Laboratorio de Micología y Fitopatología
Universidad de Los Andes, Colombia
[http://bioinf.uniandes.edu.co]
+ 57 1 3394949 ext 2619
luisrodr at uniandes.edu.co
me at miguel.weapps.com
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