[Bioperl-l] Project: BioPerl 2.0 (and beyond)

[Robert Bradbury]

On 4/6/10, lin yu <joycelin12 at gmail.com> wrote:
> Therefore, I would like to propose the use of BioPerl in access R
> phlyogenetic tools or the combination of R and BioPerl in other similar
> applications like microarray analysis etc. Would it be possible? I would
> like to know the answer as soon as possible as I can edit my proposal in the
> case.

Joyce, it isn't clear what you are really asking for here.  I did some
digging and it appears as if "R" is a statistical language derived
from S:
http://www.r-project.org/
It isn't clear whether there is currently a toolset of phylogenetics
applications that use R (if so could you provide a pointer or some
examples)?

In theory one can interface perl programs to anything since it has
complete system call capabilities.  Presumably the advantage from a
BioPerl standpoint is to have BioPerl deal with the databases, genes,
genomes, etc. (something R presumably does not do) and have R deal
with the statistics side of any analysis.  But one needs a more
complete examination of what statistical aspects of phylogenetics
BioPerl does not currently handle (and could be better handled by
taking advantage of features which R might have).

[In my opinion currently there is already way too much overlap in
tools packages with BioPerl, BioPython and BioRuby -- and there is no
matrix regarding the capabilities or lack thereof with each of these
so one could easily tell which of the three could or should best be
interfaced to R.]

It looks as if the phyloinformatics project is here:
https://www.nescent.org/wg/phyloinformatics/index.php?title=Phyloinformatics_Summer_of_Code_2010
but it isn't clear whether there is any coordination between the
BioPerl side of things and the Phyloinformatics side of things.