[Bioperl-l] Find distances between LCA's and the other nodes from a tree
thomas.sharpton at gmail.com
Mon Oct 3 10:35:33 EDT 2011
On Mon, Oct 3, 2011 at 4:28 AM, Dave Messina <David.Messina at sbc.su.se>wrote:
In my hands, there is a Node object returned as $lca. However, it doesn't
> have an id so the next line where you try to print $lca->id, I get an
> undefined value error.
> When I look at $lca, it doesn't seems to be equivalent to node C, which,
> based on the tree you supplied, I would expect to be the LCA. SO there may
> in fact be something wrong in the BioPerl code here, too.
> However, I'm not that familiar with these modules, and I know there's been
> some recent work done on them, so perhaps someone else can chime in here.
Dave is (as usual) right: $lca is a Node object. He's also right that the
node $lca doesn't have an id. But I don't think this is a problem with
BioPerl, but rather with how the newick tree in question is formatted.
Specifically, the tree that Ross provided only has ids at the leaf nodes,
which is why $lca->id() is returning an error (the internal node ids are
Ross, you'll need to adopt the following format for your trees if you want
to call internal node ids, at least as I understand how these BioPerl
modules work. Instead of:
Structure your newick trees like this:
The above trees are identical, with the exception that the internal nodes E
and F have identifiers (names) associated with them.
Does that make sense? You might check the wikipedia page for more
information (http://en.wikipedia.org/wiki/Newick_format) and you can quickly
view both of the above trees through the web-based tool PhyloWidget (
http://www.phylowidget.org) to get a better understanding of what I'm
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