What's new ?
-Jalview Version 2.07
-Sequence Fetcher has been added to quickly - retrieve sequences with known ids from several databases.
-Sequence Features enhanced to allow - the user to display all features of a Uniprot file on the alignment and subsequently - colour, hide or show overlapping features.
-Choose to omit /start-end from sequences when - saving files. This is important for saving files to be used by some programs - which cannot read the original Jalview sequence output with the appended /start-end.
-PDB structure viewer enhanced. Mapping - between sequence and structure has been enhanced, colours on the alignment are - reflected in the structure viewer.
-Jalview Applet can read - in feature files, PDB files be used as input to HTML form See the website - to find out the new parameters available for the Applet Version of Jalview.
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Jalview Version 2.08
+Editing can be locked to the + selection area so that any edits made within the locked area do + not unexpectedly shift other parts of the alignment.
+Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list + of keyboard controls, look here.
+Create sequence features from searches. + Previously, the regions of sequences highlighted as the result of + searches were added as new regions in the alignment. Now, the sequence region + selected by a search can be used to define named sequences features + attached to the sequence, rather than the alignment. +
+Sequence feature display and rendering has also been enhanced, with + the addition of sequence feature groups (which can be used to show + or hide a set of features en masse) and user defined + feature colours as well as transparency controls, using the Sequence Feature Settings + window. The Features file + has also been extended to accomodate these enhancements.
+Alignment annotation and colouring is also considerably + enhanced. Precalculated symbolic and quantitative annotations (text labels, + secondary structure symbols and multiple scalar graphs) can now be + loaded onto alignments via the Annotation + File. Additionally, the Annotation + Colouring dialog box allows an alignment to be coloured based on + any of the graphed quantities with which it is annotated.
+Rendering speed has been improved by disabling anti-aliasing via
+ the Smooth Fonts
+ option in the View
+ menu (its default set in Preferences). In addition, response
+ times when editing alignments can be reduced by turning off the automatic
+ calculation of amino acid property Consensus (which has been
+ reintroduced to the Calculate menu as Autocalculate Consensus).
+
Issues Resolved
-Group Editing is possible with Control and mouse click. Alt key and mouse press - does not work as this translates as the middle mouse button, which since 2.04 - is now used to scroll the alignment and change the font size.
-HTML export now writes groups and features which were previously missing.
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See the Release History page for details of all new features and resolved issues.