problems loading nhx files

Still slow, even with that dataset ? What memory is being allocated … I found it fine on an i7 mac with 128mb java heap.

J. B. Procter Jalview/enfin Barton group


-----Original Message-----
From: Albert Vilella <>
To: Jim Procter <>
Sent: Thu, 09 Jun 2011 16:32
Subject: Re: problems loading nhx files

I tried with the latest version but still it’s superslow…

On Thu, Jun 9, 2011 at 3:22 AM, Jim Procter <> 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

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 :slight_smile:
I tried this on my machine using the latest build of jalview (get it from
the page), and don’t seem to have a problem.
Can you have a go with that ?


Sorry to jump in here, but this seems odd (and Jim should be having a holiday and not answering so many Jalview queries from Australia!).
I can’t diagnose this kind of thing, but maybe there is something unusual with your java or o/s setup. Have you tried it on a different computer?


Geoff Barton, Professor of Bioinformatics,  College of Life Sciences
University of Dundee, Scotland, UK.          [](
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