[Biopython] Supertree - R

[Cymon Cox]

Hi Patricia,

On 2 November 2011 10:39, Patricia Soares <patriciaseraos at gmail.com> wrote:

> Hello,
>
> I need to build a supertree from four different methods.



You want to build a supertree from a combination of optimal tree(s) of each
of 4 different tree building methods, right?



> I found a code
> able to build supertrees with R.



There is a long and complex literature about the best way to reconstruct
supertrees. But from the code you attached, you appear to be wanting to
reconstruct a supertree using Matrix Representation using Parsimony (MRP) -
basically recode the source trees as nodes present/absent in a matrix then
use parsimony to find the shortest tree.



> But I wanted to use python to do this.
> I was wondering if you have any way to do something similar to the R
> code and build a supertree.
>


I'm not aware of anything in Biopython. There is however a module in p4 (
http://code.google.com/p/p4-phylogenetics) p4.MRP. mrp(trees,
taxNames=None) that will recode you source trees and write the MRP matrix.
You can then use your favourite parsimony implementation (PAUP*, TNT, etc)
to build the tree.

Cheers, Cymon