In addition to a staggering number of bug-fixes and improvements, this major release brings new key capabilities for:

• Alignment, editing and analysis of proteins linked to coding sequences - Discovery and retrieval of 3D Structure Data from the EMBL-EBI’s PDBe query services
• Publishing and exchange of data and visualisations on the Web with BioJS-MSA.
• UCSF Chimera and VARNA session storage in Jalview Projects
• Secondary structure prediction with Jpred4.

For the full story, please check out the new version’s release notes and documentation. We’ll look forward seeing your questions and bug-reports on the mailing lists, and our bug-tracker !

Jalview 2.9 is the first major release for our Wellcome Trust and BBSRC funded team based in the University of Dundee’s School of Life Sciences, and it could not have happened without their support. We would also like to thank Swanand Gore, Jose Dana and Sameer Velankar of the EMBL-EBI PDBe for getting the PDBe search API ready for prime-time, and look forward to making use of many more BioSOLR services in the future. Finally, we wish our 2015 Summer intern, Dmitrijs Finkelberg, the best of luck in his new course. He was responsible for many of the designs for the Jalview Booth at ISMB 2015, and also created two new films about Jalview which are now available on our youtube channel.

Now the release is out, we are planning new training courses and updating our materials for version 2.9. Please contact us if you’d like a course at your institution!