What's new in Jalview 2.10.1 ?

Jalview 2.10.1 was released on 29th November 2016. Full details are in the Jalview 2.10.1 Release Notes, but the highlights are below. This is also the first release to include contributions from Kira Mourão, who joined Jalview's core development team in October 2016.

• More memory efficient
  We've slimmed down the consensus analysis data structures used by Jalview so even wider alignments can be worked with.
• Select highlighted region
  Press 'B' or use the new menu option in the alignment window's Select menu to mark columns containing highlighted regions generated from structure selections, mouse-overs, or resulting from a Find operation.
• New custom link mechanism for opening URLs for database cross references.
  If you have customised URL links in your Jalview preferences, then you may already have seen the warning dialog (see below).
• New command line export option for BioJS MSAviewer
  A number of small bugs with the HTML export functions from the Jalview desktop were also fixed.
• Small but significant changes to the physicochemical properties and consensus calculations
  Threonine is no longer considered a non-hydrophobic residue in the protein conservation calculation, and minor bugs addressed in PID and consensus colouring.
• Correct display of disulphide bond features
  In linked structure views, Jalview would highlight all residues between in addition to the two linked cysteines. The 'select columns by feature' function in the feature settings would also select all intermediate columns.

Warning dialog about updating your configured URL links
In the desktop prior to Jalview 2.10.1, the only way to configure custom links for a particular database cross-reference for a sequence was to give it a name that exactly matched the database source, and a regular expression for filtering out any spurious matches generated when the custom linked was tested against the Sequence's ID string. Since the introduction of the $DB_ACCESSION$ token, however, $SEQUENCE_ID$ will not be used for database cross-reference accession strings, and if you have custom links configured, Jalview will raise a warning message so let you know that you may need to update your links to use $DB_ACCESSION$.