[Biopython] Tree Comparison in BioPython

[Eric Talevich]

Hi Zheng,

The usual way to do this is the Robinson-Foulds metric. It's not
implemented directly in Biopython yet, but two programs that can do it are
"treedist" in Phylip (a.k.a. ftreedist in Embassy, in the Debian package
"embassy-phylip"), and RAxML with the "-f r" option. The Python library
DendroPy also has a Robinson-Foulds distance function.

See:
https://groups.google.com/forum/?fromgroups=#!topic/raxml/JgvxgknTeqw
http://emboss.bioinformatics.nl/cgi-bin/emboss/help/ftreedist
http://pythonhosted.org/DendroPy/library/tree.html#dendropy.dataobject.tree.Tree.robinson_foulds_distance

Hope that helps,
Eric


On Fri, Mar 22, 2013 at 4:02 PM, 阮铮 <rz1991 at foxmail.com> wrote:

> Hi,
>
> I was wondering if there is any tree comparison support in BioPython? I
> want to know if two trees are topologically the same.
>
>
> The idea I have now is to convert trees into an adjacency matrix and check
> their equality. This is not easy because internal node typically don't have
> a name and the structure of the adjacency matrix may be different. Or I may
> go through all internal nodes and check if they have the same terminals.
> This idea is also not straightforward as typically for an internal node in
> one tree I have to compare it against all the internal nodes in the other
> tree to potentially find a match.
>
>
> Is there any suggestions? Thanks!!
>
>
> Best,
> Zheng
>
>
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