I'm slowing trying to get phylogenies into the wiki that I'm playing with. Here's an early example, the TreeBASE tree T6002, from the study A Phylogenomic Study of Birds Reveals Their Evolutionary History. The tree is displayed using my tvwidget. Below are listed the OTUs in the tree in a crude table. The idea is that this table will contain a mapping between OTU labels and taxa.

It's Friday, so time for some random, half-baked ideas. Imagine that we have a database of evolutionary trees, and these overlap for a set of taxa that we are interested in. How do we summarise these trees? One approach is to make a supertree. It would be useful to display the subtrees that went into making this supertree, if only to give an idea of how much they agree with the supertree. How to do this?

Another issue I'm trying to get my head around is how to deal with labels in phylogenies. These can be any number of things, such as GenBank sequences, specimen codes, taxon names, abbreviations of taxon names, laboratory codes, etc. Here's my quick attempt to model these: This sketches various levels of indirection to go from a label in a tree to a taxon name.

Last night BBC One aired David Attenborough's Charles Darwin and the Tree of Life, which featured a lovely "fly through" the tree of life: In conjunction with the TV show, the Wellcome Trust has launched the Interactive Tree of Life, a Flash-based view of the tree of life. There's also a blog about the project. Here's a demo of the tree: The tree looks very nice, and a lot of work has gone into it, but I am somewhat underwhelmed.

Last week I was at NESCent's 2008 Community Summit. As part of that meeting a few of us had a breakout group on "Biodiversity and phylogenetics". Brian O'Meara took some spectacularly thorough notes, including the pithy: S[wofford]: What? Julia Clarke and I were advocating data mining, not entirely successfully.

Rich Glor brought dechronization to my attention. This is a very active blog "by junior academic scientists whose research focuses on evolution, reconstruction of phylogenetic trees, and comparative methods." There's some nice stuff there, including software reviews, paper appraisals, conference reports, and *cough* porn.

I've put the first version of "tvwidget" into Google Code. This is a HTML-only widget to display large evolutionary trees (you can see how my thoughts on how to do this unfolded by following my earlier posts starting with Visualising very big trees, Part V). tvwidget itself is a C++ program that takes a tree and generates the image tiles and Javascript for the viewer. It's poorly documented, I'll deal with tis once I get some time.

Alexis Stamatakis and Jacques Rougemont have released RAxML BlackBox, a prototype Web-Server for RAxML which is attached to a 200 CPU-cluster located at the Vital-IT unit of the Swiss Institute of Bioinformatics. You can upload your data and the cluster will mul it over for up to 24 hours, so typically you can analyse alignments up to 1,000 to 1,500 sequences at present.

OK, time to put my money where my mouth is. Here's a first stab at displaying big trees in a browser. Not terribly sophisticated, but reasonably fast. Take a look at Big Trees. Approach Given a tree I simply draw it in a predetermined area (in these examples 400 x 600 pixels). If there are more leaves than can be drawn without overlapping I simply cull the leaf labels.

One of the striking pictures in Tamara Munzner et al.'s paper "TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility" (doi:10.1145/882262.882291, also available here) is that of a biologist struggling to visualise a large phylogeny.