[Jalview-discuss] problems loading nhx files

Jim Procter jprocter at compbio.dundee.ac.uk
Thu Jun 9 03:22:51 BST 2011

Hi Albert,

On 23/07/28164 05:59, Albert Vilella wrote:
> I am loading alignments and nhx tree files associated to them (see
> example in attachments) with Jalview 2.4.0.b2, and I getting this
> window:
> Possible problem with tree file:
> Tree file contained comments which may confure input algorithm.
This is a warning message telling you that Jalview might not have parsed 
the comments in the NHX file correctly. Most of the time Jalview gets it 
right, but my newick tree parser has been known to get confused with 
trees with comments - however in that case, it usually results in a 
spectacularly broken tree topology, and a bunch of other problems.
> The tree loads fine, and I can sort my sequences by input tree, but
> the whole system is sluggish, it takes seconds to transition
> for every click...
ok. tree parser is working then :)
I tried this on my machine using the latest build of jalview (get it 
from the www.jalview.org/versions.html page), and don't seem to have a 
problem. Can you have a go with that ?


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