[Bioperl-l] phylip - ProtDist Problem

[Jason Stajich]

Hmm - there are some changes in PHYLIP 3.6 from 3.5 menus, did you make 
sure your PHYLIP version environment was set by setting the ENV 
variable otherwise the wrong commands are sent in.

PHYLIPVERSION=3.6

Also you are using 3.6.1 which I know has some bug fixes over 3.6 but 
may also have incurred some changes in how the menus act - I don't 
really know though.

I guess either use 3.5 or try debugging the running of 3.6.1 by putting 
some print statements in there - see what is being sent in to protdist 
and then run protdist by hand to see what are the expected menu items 
to get what you want.  That is how Shawn and I built this in the first 
place.

-jason
On Aug 31, 2004, at 9:26 PM, Nathan Haigh wrote:

> 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!?
>
> Regards
> Nathan
>
>
>
> # use seqboot to generate bootstrap alignments
> my @params_seqboot = ('datatype'=>'SEQUENCE', 'replicates'=>100);
> my $seqboot_factory =
> Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params_seqboot);
> 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");
> $outtree->write_tree($tree);
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu