[Bioperl-l] Bio::TreeIO, Root-tip branch lengths

Mark A. Jensen maj at fortinbras.us
Sat Nov 14 16:47:37 EST 2009

Hi Jun,

Some hints: incorporate

@leaves = $tree->get_leaf_nodes;


use Bio::Tree::TreeFunctionsI;
$distance = $tree->distance( $node_a, $node_b );

cheers, Mark

----- Original Message ----- 
From: "Jun Inoue" <j.inoue at ucl.ac.uk>
To: <bioperl-l at lists.open-bio.org>
Cc: "井上 潤" <j.inoue at ucl.ac.uk>
Sent: Saturday, November 14, 2009 2:20 PM
Subject: [Bioperl-l] Bio::TreeIO, Root-tip branch lengths

> Dear All,
> I just started to learn BioPerl for phylogenetics.
> Usually I am using perl v5.10.0 on my Mac OS 10.5.8.
> I would like to ask you a hint to calculate the Branch lengths
> from root to tip for all species in NEWICK TREE format.
> Please see the following web site.
> I am explaining what I want to do and
> showing my easy script (not completed).
> http://www.geocities.jp/ancientfishtree/BioPerl_BLRootTip.html
> Thank you for your help.
> Best,
> Jun Inoue
> http://www.geocities.jp/ancientfishtree/index_eng.html
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> Bioperl-l at lists.open-bio.org
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