[BioPython] Phylogenetics trees

[Rick Ree]

On 29 Aug 2000, Brad Chapman wrote:

> > Rick Ree wrote:
> > Hi folks.  I've been away for 2 months and have just seen this series
> >  of posts.	Mavric's code is available for perusal and re-use, and
> I'd be
> >  happy if it could benefit BioPython in some way.  
> >  Please tell me how I might contribute the code to BioPython, and if
> >  this would be useful. 
> 
> I personally would be really happy to see Mavric code in BioPython! Greg
> just posted his code to parse and work with Newick Trees a few days back
> -- I think it would be really great if you both could come together on a
> single set of modules to do this kind of stuff that we could work in
> BioPython. I'd also be willing to lend a hand on this as well, although
> I am still quite green in phylogenetic analysis stuff. If you and Greg
> think this is a good idea, I think you, Greg and I (and anyone else who
> is interested!) could hash out a plan either by e-mail or wiki, and then
> go forward with it. Let me know what you all think about this. 

I forgot to include the URL to Mavric:

http://www.bioinformatics.org/mavric

It can also parse and write newick-formatted tree descriptions, and many
tree manipulation functions are available or easily written.  I'd be glad
to help in designing a module for BioPython, but I'm not sure what sort of
functionality would be most useful to BioPython users (I work on Mavric to
scratch my own itch, so to speak :)  I guess that is what we could talk
about.

--Rick