[Jalview-discuss] Jalview-discuss Digest, Vol 45, Issue 2

Jim Procter jprocter at compbio.dundee.ac.uk
Tue Sep 13 09:30:41 BST 2011

Hi David.

On 12/09/2011 19:05, David M. Goodstein wrote:
> It would be nice to have NHX capabilities, so we can annotate the 
> various nodes and work with arbitrary length names.
Jalview's tree viewer doesn't support any NHX annotations, but the 
parser does support quoted node names and preserves all node comments 
within the tree datamodel, so they are there if you want to parse them out.

Unfortunately, when I was working on it, I didn't have a comprehensive 
set of NHX files to test the parser with, and instead left in checks 
that will raise a warning dialog if the tree file contains NHX 
annotations to warn the user that there may be problems. If you know 
(and trust) the source of the file, however, then it should be possible 
to safely squash that error within the JABAWS phylogeny service web 
service client.

What NHX annotations are you interested in using ?   It's of course 
possible to extend Jalview to cope with anything, but we should 
seriously consider if it will be more efficient to  incorporate 
Archeopteryx, if you need full NHX capabilities.


ps. Everyone on this thread is now subscribed to the jalview-dev list, 
so we should move further discussion there.

pps. arbitrary length node names are only important if you are importing 
trees from outside of Jalview. Normally, any sequences sent to a service 
have an autogenerated ID string, and jalview replaces the ID with the 
displayed sequence name when the results are retrieved.

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