[Biopython] Bio.Phyo.Consensus

[Eric Talevich]

On Wed, Sep 25, 2013 at 6:25 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Wed, Sep 25, 2013 at 1:14 PM, Jessica Hedge <jesshedge at yahoo.co.uk>
> wrote:
> > Hello,
> >
> > I'm trying to use the Bio.Phylo.Consensus module in order to
> > simulate bootstrap replicates of a multiple sequence alignment.
> > I have both Biopython (version 1.61) and Phylo module
> > installed but the Consensus module doesn't seem to exist.
> >
> > Is the Consensus module available in another version of Biopython?
> >
> > Many thanks,
> >
> > Jess
>
> This is probably a question for Eric (CC'd explicitly).
>
> There isn't currently a module with that exact name
> under Bio.Phylo, but the wiki does mention it - so this
> is probably just an out of date example reflecting
> non-final code: http://biopython.org/wiki/Phylo
>
> Peter
>

Ah, sorry for the confusion -- the Bio.Phylo.Consensus function and most of
the other things on that page starting at the "Tree Construction" section
refer to Yanbo Ye's development branch for Google Summer of Code, which
just completed. You can get a copy of this code here:
https://github.com/lijax/biopython

The work is not yet merged into the main Biopython source tree, and some
parts of it could potentially change in the near future.

I'll add a note to this effect on the wiki.

-Eric