[Biojava-l] New idea for alignment parsing and Re: Parser for MrBayes output

Jose Manuel Duarte jose.duarte at psi.ch
Thu Nov 6 11:19:45 UTC 2014

Hi Ben

Thanks a lot for all the insights. I am really not the most appropriate 
person to comment on all the biojava phylogeny and sequence related 
things but anyway below are some of my opinions.

On 05/11/14 17:22, Ben Stöver wrote:
> The more interesting/urgent thing though might be parsing the consensus tree
> which is in Nexus format (or writing the input files for MrBayes). Although
> the Nexus format is not really state of the art anymore and replacements like
> e.g. NeXML (http://nexml.org/ )  - which overcome its limitations - should be
> prefered if you implement a new software, the Nexus format is still widely
> used and supporting in BioJava 3 (or 4) would surely be a good idea. There was
> a extensible Nexus parser in BioJava 1.x
> (http://www.biojava.org/docs/api1.9.1/org/biojavax/bio/phylo/io/nexus/package-summary.html
> ) which could be ported to BioJava 3 (4). (This has never been done until now,
> hasen't it?)

If I understand it properly they were not ported yet to 3 because of 
lack of time, so I think the porting of the nexus stuff would be a great 
thing. +1 to that.

> Therefore I would offer to implement such functionality for BioJava, but
> before making a pull request or anything, I wanted to ask for opinion of the
> cummunity on that idea and also if I might have missed concepts in BioJava
> that would currently already allow to do something similar.

To me the whole idea sounds great. Especially if it can be made 
compatible with the existing Biojava interfaces. If I understand what 
you propose, you would only introduce a new way of parsing things which 
could even live alongside the current parsers. It could even go to its 
own package (sequence.nio ?). For me this is a +1 too.



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