[Bioperl-l] Phlip

[Jason Stajich]

So you are getting a tree back though when you pass in the matrix
properly? Isn't possible total_branch_length is failing - what happens
when you do this?

for my $node ( $tree->get_leaf_nodes ) {
 print $node->id, " ", $node->branch_length, "\n";
}

-jason

On Fri, 25 Jun 2004, Jonathan Manning wrote:

> Hi all,
>
> Was hoping Jason or someone else could nudge me in the right direction
> with Phylip. I was having trouble with the suite and tree drawing, and
> think I've narrowed it down to Neighbour, since the output tree has 0
> 'total branch length'. I believe Protdist is creating the matrix
> correctly, since get_column returns a sensible-looking list of values.
> My snippet of code is:
>
> my ($matrix)   = $protdist->run($alnmnt);
> 		print "Number of rows in matrix: ", $matrix->num_rows(), "\n";
>         my @n_params = (
>             'type'     => 'NJ',
>             'outgroup' => 2,
>             'lowtri'   => 1,
>             'upptri'   => 1,
>             'subrep'   => 1
>         );
>         my $neighbor =
> Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@n_params);
>         my ($tree)   = $neighbor->run($matrix);
> 		print $tree, "\n";
> 		print "Total branch length: ", $tree->total_branch_length(), "\n";
>
>
> The documentation actually states that a matrix argument should be a
> hash reference, but if I create a reference and pass it in like:
>
> my $matrixref = \$matrix;
>
> I just get this message:
>
> Can't call method "isa" on unblessed reference at
> /usr/lib/perl5/site_perl/5.8.3/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
> line 458.
>
>
> Would be very grateful for any help anyone could offer!
>
> Jon
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu