Adding branch lengths

[Yan Wong]

I'm using Bio::Phylo to read in a Newick tree without branch lengths. If I call ultrametricize(), perhaps unsurprisingly I get errors:

Use of uninitialized value in addition (+) at /Library/Perl/5.16/Bio/Phylo/Forest/TreeRole.pm line 2265.

What's the easiest way to assign a default length to all the branches on the tree, before calling ultrametricize()? 

p.s. I might also have a hacky Newick tree where only some of the branches have lengths. In this case I'd want to assign a default length to any nodes that don't have a length already.

[Rutger Vos]

What default value do you have in mind? E.g.:

$value = 1;

$tree->visit(sub{

    my $node = shift;

    $node->set_branch_length( $value ) if not defined $node->get_branch_length;

});

...now all undefined branch lengths have been set to 1.

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[Yan Wong]

On Thursday, 26 June 2014 13:15:26 UTC+1, Rutger Vos wrote:

$tree->visit(...

Ah, tat's what I was missing. Ideal, thanks for the quick reply.

Yan