What's new ?

Highlights in Jalview Version 2.5

Linked viewing of nucleic acid sequences and structures
Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
Order an alignment by sequence length, or using the average score or total feature count for each sequence.
Shading features by score or associated description
Subdivide alignment and groups based on identity of selected subsequence (Make Groups from Selection).
New hide/show options including Shift+Control+H to hide everything but the currently selected region.

Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources and RFAM.
Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
Group-associated consensus, sequence logos and conservation plots
Symbol distributions for each column can be exported and visualized as sequence logos
Jalview Java Console
New webservice for submitting sequences and IDs to Envision2 Workflows
Improved VAMSAS synchronization and sharing of selections.
New Purine/Pyrimidine colour scheme.
Colouring of RNA secondary structure by helices. See Nucleic Acid Support.

Middle button resizes annotation row height
New Parameters - including default tree display settings.
Non-positional features displayed in ID tooltip

Issues Resolved (a select list)

Source field in GFF files parsed as feature source rather than description
Non-positional features are now included in sequence feature and gff files (controlled via non-positional feature visibility in tooltip).
URL links generated for all feature links (bugfix)
Codons containing ambiguous nucleotides translated as 'X' in peptide product
Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.
Jalview Annotation File generation/parsing consistent with documentation (e.g. Stockholm annotation can be exported and re-imported)
Find incrementally searches ID string matches as well as subsequence matches, and correctly reports total number of both.

Desktop Issues
Better handling of exceptions during sequence retrieval
PDB files retrieved from URLs are cached properly
Sequence description lines properly shared via VAMSAS
Sequence fetcher fetches multiple records for all data sources
Ensured that command line das feature retrieval completes before alignment figures are generated.
Reduced time taken when opening file browser for first time.
User defined group colours properly recovered from Jalview projects.

See the Release History page for details of all new features and resolved issues.