[Bioperl-l] Summer of Code project idea: build-out of PopGen::Simulation::Coalescent

[Mark A. Jensen]

Hi  all--

With apologies to Jason, I took the liberty of throwing out an
idea or two re the BioPerl coalescent implementation
as a NESCent Summer of Code project. The underlying
motivation is to make the module more immediately useful
to infectious disease evolutionists, and also to lay a foundation
for a coalescent API (and who couldn't use another coalescent
API?). The main conceptual addition would
be writing routines to implement the so-called serial coalescent,
which is a natural modification of Hudson's algorithm that
allows for specification of the time of the sample, as well
as the size and mutation rate.

Rather than reproducing the entire screed, I direct interested
folks to the following

https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009#Building_out_BioPerl_PopGen::Simulation_modules_for_infectious_disease

If this is interesting to you (as a student or as a co-mentor), please reply here,
respond in the phylosoc at nescent.org list, or contact me directly.

cheers all-
Mark