[Bioperl-l] problems parsing interlevaed phylip file with Bio::AlignIO

[Hannes Hettling]

Dear all,

I am having trouble reading in an interleaved phylip file. It works with a 
smaller example, but not with the file attached to this post (93 taxa, 
36338 sites). 

Here is my code:

    use Bio::AlignIO;
    my $in  = Bio::AlignIO->new(-file   => 'myphylip.phy' ,
                            -format => 'phylip', 
                            -interleaved => 1,
                            -idlength => 10);

    while ( my $aln = $in->next_aln() ) {
            print "Alignment found!\n";
            print ref ($aln)."\n";
    }


The variable $in is a Bio::AlignIO::phylip object, as expected. The phylip 
file seems to be valid, I was able to convert it to fasta (using 
http://sequenceconversion.bugaco.com/converter/biology/sequences/phylip_to_fasta.php) 
and then I could read the fasta with AlignIO.

Does anyone have an idea what I could me missing?

Many thanks in advance,

Hannes

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