[BioPython] Phylogenetics trees

[Greg and Lisa]

When I wrote my tree classes, I was unaware that Mavric existed. It is
pretty much exactly where I wanted my project to be in the near future, and
I don't think my own code offers any additional benefits. If Rick is willing
to allow Mavric to be a part of BioPython, I think it should probably just
replace my code. One thing that I can offer is the GUI that I'm working on,
which uses Tkinter, and should be more portable than Rick's GUI. It's still
in the (very) early stages of development, but it should be very easy to
switch over to the Mavric classes (since they are very similar to my
own--great minds think alike!)

    - Greg

> > 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
>
>