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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