I drilled down into the Group by Tree function to see why it seems slow.
With an alignment of 50 sequences x 1800 (I'm using Mikk Puustusmaa's DNA data), if you click 'deep' in the tree (so creating many groups), the refresh with group colouring takes over a second (Jalview desktop 2.8.2). It turns out most of the time is spent in SequenceGroup.recalcConservation(). This takes around 13ms but is done for each group. For example: - 82 groups formed - time in recalcConservation: 82 * 13ms = 1066ms approx - total time in colourGroups: 1111ms This gets more noticeable in a split frame view when there are two alignments performing this action. Not sure if there are any easy optimisations here. ? It still happens with no annotations displayed, and Puridine/Pyrimidine colour scheme, which feels unnecessary...? Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology College of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096
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