[Bioperl-l] Phlip

Jonathan Manning bmb9jrm at bmb.leeds.ac.uk
Fri Jun 25 09:36:19 EDT 2004

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 $neighbor =
        my ($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
line 458.

Would be very grateful for any help anyone could offer!


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