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

Spencer Bliven sbliven at ucsd.edu
Thu Nov 6 11:52:13 UTC 2014


This sounds like a great idea and a really useful addition to biojava! I
would lean towards only parsing the consensus tree, as the other formats
are pretty specific use cases. We're sure forester doesn't provide Nexus
parsing, right? The documentation isn't particularly complete, but it's
already a phylo dependency so we should avoid duplicating any features.

As to your second suggestion, it sounds very similar to how FastaReader
currently works, with the user providing a SequenceCreator which
instantiates whatever Sequence implementation you want to use. Mutable
sequences can lead to a host of additional problems, which is why the
sequences are currently generated atomically. Or am I misunderstanding your

It would be fantastic to have some additional development of multiple
alignments and the phylo package! Thanks for the offer to contribute!


On Thu, Nov 6, 2014 at 12:19 PM, Jose Manuel Duarte <jose.duarte at psi.ch>

> 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.
> Cheers
> Jose
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