[Bioperl-l] problem with neighbor.pm

Elizabeth Williams ew9 at york.ac.uk
Wed Feb 4 05:11:29 EST 2004


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 
STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::_run 
STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::run 
STACK: Bio::Tools::Run::Phylo::Phylip::Neighbor::create_tree 
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' => 
                         my $factory = 
                         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 = 

                         my $matrix = $protdist_factory->run($aln);

                         my @params_neighbor = ('type'=>'NJ');

                         my $neighborfactory = 

                         my $tree = $neighborfactory->create_tree($matrix);

Elizabeth J.B. Williams

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