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

David M. Goodstein dmgoodstein at lbl.gov
Fri Sep 16 21:38:27 BST 2011

On Sep 13, 2011, at 1:30 AM, Jim Procter wrote:

> 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.

If we can support long names, bootstraps, and the ability to provide  
URLs to crown nodes with the current Jalview version of newick, there  
probably isn't any need to go to NHX.


> Jim.
> 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.

David M. Goodstein, Ph.D.
Phytozome Group Lead
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
Center for Integrative Genomics - UC Berkeley

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