[Bioperl-l] Alignment works with codeml (not loading in bioperl)
Munirul Islam
ba6450 at wayne.edu
Thu Jul 26 19:21:20 UTC 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
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: seq.txt
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20070726/7c180f0b/attachment-0004.txt>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: seq.out
Type: application/octet-stream
Size: 24318 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/bioperl-l/attachments/20070726/7c180f0b/attachment-0004.obj>
More information about the Bioperl-l
mailing list