[Bioperl-l] GSoC 2011

[Fei Hu]

Hi, All.

My name is Fei Hu from U. of South Carolina. I am currently a second-year
Ph.D student in computer science focusing on gene order and sequence(DNA &
AA) phylogeny as well as whole genome alignment. I am instreseted in joining
bioperl project of GSoC 2011. I have two ideas that would like to share.

My first idea is to extend the bioperl so that it can process and analysis
gene order data using published package such as MGR, GRAPPA and distance
estimator. This is a relatively new type of data and many great researchers
have contributed to this type of phylogeny reconstruction (Dr. Pavel Penzer,
Dr. Bernard Moret and Dr. David Sankoff).

Secondly as maximum likelihood becomes more and more popular, especially
RAxML has been widely recognized and used(over 1000 citations). I think it's
time to integrate that as well as GARLI into the Bio::Tools. I extensively
used and explored RAxML in my last publication on gene order phylogeny.

Those are just my preliminary thoughts, not even a plan and any suggestion
is greatly appreciated!!! I use perl on daily bases for data processing and
composing testing scripts, but not much OOP involved.

PS: Rest api for CIPRES is no longer available. So this following task can't
be finished right now:
Development of a
Bio::Tools::Run::RemoteBlast<http://bioperl.org/wiki/Module:Bio::Tools::Run::RemoteBlast>-like
interface to CIPRES remote analyses; for more see this
thread<http://thread.gmane.org/gmane.comp.lang.perl.bio.general/16524>
.

And Thank you all.
Best

Fei

-- 
*Fei Hu
Bioinformatics Lab
3D-11 Swearingen Building
U of South Carolina
Tel: 803-397-5240*