During the past few weeks a lot of features have been added and improved in GenomeView and JAnnot. Most of the intermediate versions have only been made available internally in the SVN, but I think it's time for another public release. There are three notable changes from version 1.90. First the GUI is reorganized to be easier to use. Second, we have added support for short read (RNA-Seq, Chip-Seq, etc.) data Next-generation sequencing can now be visualized with GenomeView. And third, we have added support for authentication and SSL to ensure secure transfer of your data.

Download latest version of GenomeView and JAnnot
The preferred way to launch is still the web start you find in the top-left corner of the site.
JAnnot 1.96 API docs

A non-exhaustive list of improvements, changes and new features that found their way into GenomeView in the past few months is provided in the rest of the announcement.

GenomeView changes

• Improved search and added overlap search
• Improved gene structure track
• Improved feature track
• Improved multiple alignment track: faster, less memory and better visualized
• Improved keyboard navigation
• New navigation panel, inspired by Argo2
• Multi-threaded track loading
• Removed BioMoby support
• Removed chromosome view
• Major GUI reorganization to accommodate removed and added features
• Fixed a bunch of bugs and glitches
• Added basic support for Distributed Annotation Servers (DAS)
• Added short read support
• Added support for authentication and SLL
• Added caching to URLSource which makes it more efficient to retrieve data from the network

JAnnot changes

• Added a top-level object called EntrySet
• Improved detection of start and stop codons
• Fixed bugs in a number of parsers
• Added parsers for these formats and programs: PTT, TransTermHP, GeneMark, BroadSolexa, MapView and BAM/SAM
• Made Sequence and MultipleAlignment significant more memory efficient
• Improved handling of loading multiple sequences at once
• Improved multi-threaded behavior