[Biopython] More efficient neighbor joining algorithm to build phylogenetic tree

[Jing Lu]

Peter Cock <p.j.a.cock <at> googlemail.com> writes:

> 
> On Sat, Oct 19, 2013 at 4:16 PM, Jing Lu <ajingnk <at> gmail.com> wrote:
> > Hello!
> >
> > I am trying to build a large tree (~10000 nodes) from a distance matrix 
by
> > neighbor joining algorithm. I just modify the existing code from:
> > 
https://github.com/lijax/biopython/blob/master/Bio/Phylo/TreeConstruction.py
> > .
> >
> 
> Does it have to be in pure Python?
> 
> Whenever I've needed a large tree with 1000s of sequences
> I have used a fast C implementation, with bootstrapping.
> 
> Peter
> _______________________________________________
> Biopython mailing list  -  Biopython <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
> 
> 

What is the implementation you use to build a large tree?


Thanks,
Jing