[Biojava-dev] phylo code

[Richard Holland]

Hi Thasso.

Thanks for your interest! We always welcome all contributions of code and
documentation to the BioJava project.

Our GSOC project is well under way and has a plan as you have already
noticed. The items on that plan are what was agreed with our student, Boh
Yun Lee, and will be implemented by the time that GSOC is over (early
September) - or at least, most of them will, and any that aren't will be
flagged as such.

If you have suggestions to make about code already committed, we would
welcome them. Such feedback is a necessary part of the development cycle.
Likewise we would welcome contributions of code not already mentioned as
being planned on the GSOC pages.

However, if your existing code implements something that is on the to-do
list on the GSOC page, then the best thing would be to hang on till the
end of the GSOC project then contribute any items that did not get
implemented.

cheers,
Richard

On Wed, August 1, 2007 6:19 pm, Thasso Griebel wrote:
> hi,
>
> i recently explored the phylogeny code base in biojava. I am
> currently working on a phylogeny framework similar to mesquite
> (http://www.bio.informatik.uni-jena.de/epos) and i would like to add
> some functionality using biojava (the sequence stuff and the nexus
> parser).
>
> I saw the PhyloSOC07 page ( http://biojava.org/wiki/
> BioJava:PhyloSOC07 ) and i might be able to help out with some of the
> methods, so is there a way to contribute ? Or is this closed to
> participants of the google summer of code ?
>
> I have code for n-consensus and adams consensus methods and some
> possible extensions for UPGMA (provide other distance computations,
> i.e wpgma, sigle linkage and complete linkage) and NJ ( outgroup and
> rooting support ). As our research groups has a focus on supertree
> construction, we have java implementations for several graph based
> supertree methods (aho's build, mincut, modified mincut, ranked tree,
> ancestral build).
>
>
> Regards,
>
> Thasso
>
> --
> Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer Bioinformatik
> Office 3426--http://bio.informatik.uni-jena.de--Institut fuer Informatik
> Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet Jena
> Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, Germany
>
>
>
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>


-- 
Richard Holland
BioMart (http://www.biomart.org/)
EMBL-EBI
Hinxton, Cambridgeshire CB10 1SD, UK