GeneTrees: how do I read them? And can I view alignments using Jalview?

If you have clicked on the GeneTree link in Ensembl (for example, the gene tree for IL2), you may have noticed that we have a new way of displaying large GeneTrees. This time, if you have a large gene family with lots of genes that you want to look at, you won't need to ask the Miami Dolphins to let you plug your laptop into their huge screen...


This new feature in EnsemblCompara is called collapsible subtrees and allows for more compact, summarized views of interesting gene families like PAX2/PAX5/PAX8:

http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?g=ENSG00000075891

If you check the legend at the bottom, you will see that "blue triangles" correspond to collapsed subtrees that have within-species paralogs of your gene. If you want to see all the within-species paralogs expanded, you can click on the option "View paralogs of current gene". You can even set that as a default if you want in the "Configure this page" options.

Jalview is a great way to view protein alignments in the tree. And were is my Jalview link now? Click on any internal node (square) in the tree, and be able to visualize the alignment (or subalignment) with the new Jalview applet by clicking on the Jalview link. You have to have Java installed though, or the link won't show. The two Jalview windows that pop up are one, the protein alignment and the other, the underlying TreeBeST tree. You can now use Jalview's sorting feature to sort your sequences according to the tree with: Calculate->Sort->By Tree Order->URL. Having the tree associated to the alignment allows for a more phylo-centric visualization of sequence conservation: if you click at a point in the tree, a red vertical line will appear that divides the alignment into different groups. If you choose Colour->Percentage Identity, the shades of blue will be relative to the subgroups in your tree (e.g., fish versus placental mammals). This is also useful to spot segments in the alignment that don't look that good, or gaps created in a subpart that can now be collapsed in the subalignment (Edit->Remove Empty Columns), or sequences that stand out as long branches in the alignment (View->Overview Window).


For even more tree funkiness, you can use PhyloWidget to visualize our NHX trees. Use our NHX tree ("Configure this page->Output for normal tree->NHX->Save and Close->Gene Tree(text)") to copy+paste the representation of the GeneTree into Phylowidget, with duplication/speciation events (red/blue), bootstrap values (greyscale) and taxonomy levels "View->Rendering->Show clade labels". Then use the "Zoom in/Zoom out" features, or clicking on an internal node, the "Tree Edit->collapse", and specially the "View->Branch lenghts [x]" and the "View->Layout->Options->Branch Scaling" options.


We hope these new features will help you in your research. We have some new ideas that we are currently testing to visualize even more phylogenetic information, and help make better judgement on the orthology and paralogy relationships in our EnsemblCompara GeneTrees. Stay tuned for more updates!