Re: [Seqan-dev] PISA toolbox code

[Marcel Schulz <maschulz@andrew.cmu.edu>]

Am 27.01.12 09:10, schrieb John Reid:
> Hi,
>
> I've recently become interested in variable order Markov chains. I 
> plan to develop some algorithms that extend and use these chains. I've 
> been using the SeqAn library for a while now and I wonder if there are 
> any plans to release the source code for the PISA toolbox.
>
> Regards,
> John Reid.
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
Hi John,
I am the developer and maintainer of the code. Although I havent been 
working on the code for some time I know that it compiles with the most 
recent version of the library and I always had the plan to release the 
source code and make it an integral part of the library. Similarly I 
wanted to release the source code for the applications that belong to 
the PISA toolbox.
A this is a huge code base this integration will take a considerable 
amount of time and it is hard for me to say how long exactly it will 
take but I am aiming to integrate it into the library in the next months.

However, I am more than happy to send you the code for everything by 
mail if you contact me offline of this list. Furthermore I am also happy 
to answer any questions regarding possible extensions or which features 
are contained in the implementations already.
A good overview of the principal functionality can be seen from the 
documentations of the applications in the PISA toolbox, which provide 
basic learning, save/load, and likelihood estimation functions for 
different variable order markov chain estimators.

Regards,
Marcel

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Marcel H. Schulz
Ray and Stephanie Lane Center      email: maschulz@cs.cmu.edu
for Computational Biology
Carnegie Mellon University
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http://www.cs.cmu.edu/~maschulz/
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