[Biopython-dev] PopGen status and new developments

[Giovanni Marco Dall'Olio]

On Wed, Nov 12, 2008 at 7:02 PM, Tiago Antão <tiagoantao at gmail.com> wrote:
> Hi,
>
> This an email with the status of current PopGen developments. In some
> points, advice is especially welcome.

Hi Tiago!!
Have you noticed (I thought it wasn't directly related to PopGen so I
didn't tell you directly) about this parser for fastPhaseOutput?
- http://bugzilla.open-bio.org/show_bug.cgi?id=2643

>
>
> 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).
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>



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