[Bioperl-l] Alignment works with codeml (not loading in bioperl)

Munirul Islam ba6450 at wayne.edu
Thu Jul 26 15:21:20 EDT 2007


Hello Everyone:

I have an alignment ('seq.txt').  It runs fine when I directly run codeml.  But when I try to load the alignment in bioperl, I get an error saying that the sequence is not interleaved.

my $alignio = Bio::AlignIO->new(-format => 'phylip',
				-file   => 'seq.txt');

I guess its not in valid phylip format.

I tried to change 'seq.txt' to sequential format.  Still that didn't work.

Any suggestions on how to load 'seq.txt' in bioperl?  

Thanks,

Munir
PhD Student
Computer Science
Wayne State University
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