Hi Albert,
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 ?
Jim.
···
On 23/07/28164 05:59, Albert Vilella wrote:
I tried with the latest version but still it's superslow...
···
On Thu, Jun 9, 2011 at 3:22 AM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
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 ?
Jim.