[Biopython-dev] PopGen status and new developments

[Bruce Southey]

Peter wrote:
> Tiago Antão wrote:
>   
>> 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?
>>     
>
> Assuming the tools are useful, then I have no objection to including
> command line wrappers for them in Biopython.
>
> I'm not 100% sure what you meant by "supporting an application like
> this", but if you are asking about supporting these cross-platform
> ports of the actual command line tools, then I don't see that as
> something Biopython should be doing.
>
> Peter
>
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>   
Hi,
I do have concerns about usefulness with regards to Biopython.

How widespread is the application?
What platforms is it released under (DOS only or some version of windows 
version like XP or Vista or Windows 7)?
Is the application well supported and will it continue to be supported?
Under what terms is the application 'free'?
How does this integrate into your ideas for Popgen?
Would it work like say clustalw where you output something from 
Biopython, run the application and perhaps import something back into 
Biopython?

If the application requires major data formatting then you would have to 
determine if it is easier to support the application or integrate it 
into Biopython. Obviously, this latter requires a clean room 
implementation of the application or the essential algorithm. Also, you 
can only provide the specification and can not be involved the actual 
implementation.

Bruce