On Monday 18th February, Jim Procter gave the opening talk at the Scottish Phylogeny Discussion Group meeting, which was held at the James Hutton Institute in Invergowrie - just a little further up the Tay from Dundee. The program for the afternoon also included some great talks from Rosanna Alderson (John Mitchell's group in St. Andrews), Cristiane Calixto (John Brown's group in JHI & U. Dundee), and Frank Wright of BIOSS (Biomathematics and Statistics Scotland).
In his talk, Jim described the ways that Jalview helps researchers create, curate and analyse nucleotide and protein multiple sequence alignments, highlighting some of its most useful features (e.g. database reference and annotation, alignments linked to trees and structure views), and new developments such as RNA secondary structure visualization. He also pointed out some of the areas where Jalview could be doing a bit better - particularly when handling phylogenetic data and working with codon alignments. Most of Jalview's deficiencies could be fixed with new parsers (PHYLIP and NEXUS support, for instance), but Jalview would also benefit from the addition of phylogenetic analysis services to JABAWS system. There's also scope for extending Jalview's alignment visualization system so that it displays the amino acid translation for cDNA in a nucleotide multiple alignment, so users can analyse both protein and coding nucleotide data at the same time.
Most of these topics would make a great student software development project (and some may even be good for a bioinformatics project too!). Luckily, Google announced that the Google Summer of Code will be running again this year, and since we hope to again participate under the umbrella of the NESCent Phyloinformatics Summer of Code organisation, if you are interested in adding new support for cDNA/Protein translations, creating or interfacing with phylogenetic data and analysis services, or extending Jalview's user interface to better support phylogenetic analysis, then get in contact via the jalview-discuss mailing list.
Use the following link to download the SPDG Jalview presentation as a PDF.