[Bioperl-l] problem with neighbor.pm

[Jason Stajich]

phylip 3.5 or 3.6? -- you may need to twiddle one setting if you are using
phylip 3.6


-jason
On Wed, 4 Feb 2004, Elizabeth Williams wrote:

> Hello,
>
> I am trying to run the phylip modules on a set of Bio::seq sequences.  I
> have run into a problem with neighbor.pm  The module runs the program but
> then loses the tree somehow and comes up with this error message.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: neighbor did not create tree correctly (expected /tmp/lHCvy7ByeN/treefile)
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Root/Root.pm:328
> STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::_run
> /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:412
> STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::run
> /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:353
> STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::create_tree
> /biol/programs/perl580/lib/site_perl/5.8.0/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm:370
> STACK: geneorigin.pl:74
> -----------------------------------------------------------
>
> The script I am using is below.
> Anyone have any ideas what is causing the problem?  I am at a loss.
>
> use Bio::DB::GenPept;
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::Tools::Run::Phylo::Phylip::ProtDist;
> use Bio::Tools::Run::Phylo::Phylip::Neighbor;
>
> #use strict;
> use Bio::SeqIO;
> use Bio::Seq;
> use Bio::AlignIO;
> use Bio::SimpleAlign;
>
> $ENV{PHYLIPDIR} = '/biol/programs/phylip/exe';
> .
> .
> .
> .
> .
> .
>                          my @params_align = ('ktuple' => 2, 'matrix' =>
> 'BLOSUM');
>                          my $factory =
> Bio::Tools::Run::Alignment::Clustalw->new(@params_align);
>                          my $seq_array_ref = \@seq_array; # where
> @seq_array is an array of Bio::Seq objects created earlier
>                          my $aln = $factory->align($seq_array_ref);
>                          my @params_protdist = ('MODEL' => 'PAM');
>
>                          my $protdist_factory =
> Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params_protdist);
>
>                          my $matrix = $protdist_factory->run($aln);
>
>                          my @params_neighbor = ('type'=>'NJ');
>
>
>
>                          my $neighborfactory =
> Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params_neighbor);
>
>                          my $tree = $neighborfactory->create_tree($matrix);
>
>
> Elizabeth J.B. Williams
>
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> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu