[Bioperl-l] Find distances between LCA's and the other nodes from a tree

Dave Messina David.Messina at sbc.su.se
Mon Oct 3 07:28:41 EDT 2011


Hi Ross,

>So, if I understand your question correctly, you should be able to use all
> of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit
> confused, is_monophyletic is something you'd call on a Tree object, not on a
> Node object, right?****
>
> But the following codes will generate errors because lca cannot be
> identified.
>

Right, but there are some compile-time errors in your code. I changed a few
things so I could get it to run:

http://cl.ly/AdzH

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.


****
>
> My ultimate goal is just to conveniently derive the information that nodes
> M and L share the same LCA O for the following tree.
>

Ok, thanks for that clarification. I think the code should be able to do
that.

Incidentally, the tree you provided in Newick format does not appear to me
to be the same tree you drew as ASCII art — is that right?


Dave



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