[Bioperl-l] phylip - ProtDist Problem

Nathan Haigh nathanhaigh at ukonline.co.uk
Tue Aug 31 07:26:53 EDT 2004

I am trying to run the following script at the bottom which takes a
SimpleAlign object and runs SeqBoot on it. I would then like to take this
output and run ProtDist, Neighbor and Consense to produce a bootstrap
consensus tree. However, ProtDist just seems to fail when it gets to this
line in ProtDist.pm:

	open(PROTDIST,"|".$self->executable);		# line 399 in the
latest version of ProtDist.pm from the CVS

I am running this on WinXP from within a cgi script and have phylip v3.61. I
have no idea why this should fail as the similar line in SeqBoot works fine!

Has anyone come across this problem or know why this might be happening!?


# use seqboot to generate bootstrap alignments
my @params_seqboot = ('datatype'=>'SEQUENCE', 'replicates'=>100);
my $seqboot_factory =
my $aln_ref = $seqboot_factory->run($aln);

# create distance matrices and construct trees using neighbor
my $protdist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new();
my @tree;
foreach my $a (@{$aln_ref}) {
	my $matrix = $protdist_factory->run($a);
	push @tree, $neighbor_factory->run($matrix);
# use consense to get a final tree
my $consense_factory = Bio::Tools::Run::Phylo::Phylip::Consense->new();
my $tree = $consense_factory->run(\@tree);

# output treefile
my $outfilename = "outtrees_ur/homologene.nh"; # unrooted tree
my $outtree = new Bio::TreeIO('-format' => 'newick',
				'-file'   => ">$outfilename");

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