[Biojava-l] Parser for MrBayes output

Jose Manuel Duarte jose.duarte at psi.ch
Wed Nov 5 11:36:19 UTC 2014

Hi Pola

Welcome and great that you want to plunge in! I don't know much about 
MrBayes myself, but the idea was to include a parser in the 
biojava3-phylo module. The module uses forester 
(https://code.google.com/p/forester/wiki/forester) as the underlying 
library to deal with phylogeny data. So the idea would be to parse the 
output into a forester data structure (most likely into 

Anyway hopefully someone with a bit more knowledge about this might be 
able to add something.



On 31/10/14 18:17, Pola Kyzioł wrote:
> Hello,
> my name is Pola and I'm currently a third year student in the 
> Theoretical Computer Science
> at Jagiellonian University. I have also interest in biology, 
> especially in the field of genetics.
> I've been searching a project connected with bioinformatics which I 
> could develop
> and next use to writing my bachelor's thesis. I've found BioJava and 
> looked at its issues -
> parser for MrBayes output seems for me to be interesting to code.
> I would like to know some details about it:
> - what data you want extracted from MrBayes' output files;
> - how the created model should look like and if appropriate modules 
> already exist.
> Thanks for your help,
> Pola
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biojava-l

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