Jalview 2.9.0b2 fixes a Desktop bug where group associated consensus and conservation annotation rows are duplicated when an alignment is partitioned by clicking on the tree viewer.
We've just uploaded the patch release for version 2.9. It addresses a dozen or so minor issues in the desktop and applet, including linked editing of cDNA and Protein alignments and exchange of alignment data embedded in HTML pages. It's also the first release distributed as a signed OSX disk image, which (should) provide trouble free installation on all Macs.
Unfortunately, due to a configuration error whilst we updated our drupal servers, the Jalview desktop and applet were unavailable for a short period of time, but are now back. We realise here at www.jalview.org that this outage will have inconvenienced many people, and we've already begun to take steps to make sure this doesn't happen again.
Thanks for your patience - and stay tuned for the next Jalview release! Version 2.8.2 is rapidly approaching beta, and should be fully released by the middle of the month !