[Jalview-discuss] Jalview-discuss Digest, Vol 45, Issue 2
jprocter at compbio.dundee.ac.uk
Tue Sep 13 09:30:41 BST 2011
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
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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