[Biopython] Supertree - R

[Cymon Cox]

Hi Patricia,

On 2 November 2011 13:20, Patricia Soares <patriciaseraos at gmail.com> wrote:

> Thank you!
> I will try with this package.
>
> By the way, do you know the difference between p4.SuperTreeSupport and
> p4.MRP?
>


It's not a method to build a supertree as such, but a way of providing
measures of support for the supertree given the source trees.


>From the docstring:


    """Supertree support measures

    Super tree support can be used to calculate a number of support
measures for a set of trees and
    a supertree. The measures can be at split level and placed on the
supertree for image production or
    at tree level with a number of summary measures.

    The support of the input trees for a supertree is measured by counting
the number of
    input trees that support(S), conflict(Q), permits(P) or are relevant(R)
with the splits in the supertree.

    Supply a supertree and the input trees used to create it. Filenames or
trees will do.
    A single supertree and a list of input trees.

    For example::

etc...


Cheers, C.




>
> Cheers,
> Patricia
>
> On 11/02/2011 11:30 AM, Cymon Cox wrote:
> > 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
> >
>
>