[bip] Mailing list for PyCogent?

[alex]

>> (3) quicktree does neighbor joining on a 4500 protein family in about
>> 3 minutes .... the version in pycogent, by estimates, is going to take
>> 48 hours to do the distance estimation before even getting to the
>> neighbor joining portion.  Any thoughts?  Is quicktree taking short
>> cuts?  There must be low hanging fruit optimizations in PyCogent's
>> EstimateDistances.  I'll look myself, but I'm also looking for some
>> discussion.
> 
> I can't comment on pycogent, but if you think quicktree is fast, provided
> you have enough memory, quickjoin could be even faster.  See:
> http://www.daimi.au.dk/~mailund/quick-join.html
> 

If you think quickjoin is fast, rapidnj could be even faster.  See:
http://birc.au.dk/Software/RapidNJ/

Alex