What's new ?

Jalview 2.9.0b1 is a bug fix release for Jalview 2.9, which has been in development since December 2014. In addition to a multitude of bug fixes and minor improvements (both small, and rather big!), it also brings major new capabilities for codon-level analysis of protein alignments and the retrieval and manipulation of structural data.

For the patches since version 2.9 was release, see the Jalview 2.9.0b1 Release Notes.

Highlights in Jalview 2.9

• Visualisation, editing and analysis of cDNA and Protein alignments
  A new Split View window allows linked protein and nucleotide sequence alignments to be viewed, edited, and analysed as one.
  cDNA alignments can also be reconstructed from protein alignments calculated by Jalview's web services, and update in response to edits in the amino acid view.
  To start experimenting with cDNA/Protein analysis, jut drop a file containing cDNA sequences which code for proteins in an existing alignment, and Jalview will do the rest.
• Enhanced Integration of UCSF Chimera
  Jalview 2.9 provides full support for the use of Chimera to view 3D structures linked to alignment views in the Jalview Desktop. We've also included support for saving Chimera sessions in Jalview project files.
  Jalview and Chimera communicate using local web server connections, which may cause firewall alerts on some systems, but has the advantage of allowing bidirectional communication. Communication between Jalview and Chimera is now much more responsive, and selected regions in Chimera are now shown as highlighted regions in the Jalview desktop.
• Interactive querying of the PDBe
  Jalview users can now browse and retrieve 3D structure data from the PDB via the PDBe Search API (Gutmanas et al 2014). Developed in collaboration with the PDBe group at EMBL-EBI, the interface allows both structured and free-text queries to be performed, and allows automatic selection of the most relevant structures for an alignment acording to a variety of criteria.
• Improved support for RNA visualisation
  Jalview 2.9 integrates the latest version of the VARNA RNA Viewer, and VARNA views can also now be stored in Jalview projects. We've also dealt with a number of lingering bugs in the VARNA/Jalview interface, including the loss of pseudoknots when RNA secondary structure is shown VARNA.
• Protein Secondary Structure predictions with JPred4
  Jalview includes a number of new features for working with secondary structure predictions from the JPred4 server. These include new popup menu actions to automatically hide insertions and highlight mutations in an alignment with respect to a Reference Sequence. Jalview 2.9's new scrollable SVG HTML export was also developed specifically for the JPred4 server.