- Multiple views on alignment
- Sequence feature editing
- "Reload" alignment
- "Save" to current filename
- Background dependent text colour
- Right align sequence ids
- User-defined lower case residue colours
- Format Menu
- Select Menu
- Menu item accelerator keys
- Control-V pastes to current alignment
- Cancel button for DAS Feature Fetching
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection
- 'New Window' button on the 'Output to Text box'
- New memory efficient Undo/Redo System
- Optimised symbol lookups and conservation/consensus calculations
- Region Conservation/Consensus recalculated after edits
- Fixed Remove Empty Columns Bug (empty columns at end of alignment)
- Slowed DAS Feature Fetching for increased robustness.
- Made angle brackets in ASCII feature descriptions display correctly
- Re-instated Zoom function for PCA
- Sequence descriptions conserved in web service analysis results
- Uniprot ID discoverer uses any word separated by '∣'
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.