[Biopython-dev] PopGen status and new developments

[Tiago Antão]

Hi,

This an email with the status of current PopGen developments. In some
points, advice is especially welcome.


A. Platform support

As Peter noticed there is no Simcoal for the Mac. In a couple of weeks
I hope to have access to a Mac in order to try to compile it. In any
case I wont be able to distribute it without getting permission from
the authors, so the problem might remain...
I am now preparing support for LDNe, an application to estimate Ne
(effective population size) from LD. This application is Dos(Windows)
only. Source code is not available to the public (but the app is free
as free beer). I've had access to the source and compiled a Linux
version, again, I don't know if the author will let me distribute it.
Question: How do people feel about supporting an application like
this? Any strong feelings against?


B. New developments

1. The above LDNe module is fully coded, and being tested by a few
people (not just me). Test code and documentation TBD but easy.
2. Genepop application support (no confusion with file format support,
which is done). Partially done and informally tested. Plan to start
with just partial support.
3. Fstat parser. Coded.


C. Statistics

An ongoing interesting discussion started on statistics. I am delayed
with doing a proposal to handle statistical processing (my bad, but I
will have some free time in the next couple of weeks and I will try to
recover). My current existing code on the subject is available on
Github (by Giovanni), but I think it will need some change (not in the
functionality, but in the architecture).