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.

I would prefer to avoid Microsoft-bashing, but today I've spent time trying to get my tree viewer to work under Internet Explorer 6 and 7, and it's hell. Here are the problems I've had to deal with: Empty DIV bug On IE 6 the top of the scrollbar overlapped the transparent area when the page first loads.

Inspired partly by the image viewers mentioned earlier, and tools like Google Finance's plot of stock prices, I've built yet another demo of one way to view large trees. You can view the demo here. On the left is a thumbnail of the tree, on the right is the tree displayed "full scale", that is, you can read the labels of every leaf. In the middle appears a subset of any internal node labels.

Black Browed Albatross Originally uploaded by QuestingBeast Today is the day Katie Davis and I are launching the Bird Supertree Project. Partly an effort to distribute the task of building the tree, partly an experiment in "open source phylogenetics", we're curious (if not anxious) to see how this works out. We encourage anybody who is interested in constructing big trees to visit the site, grab the data and have a play.

For the "to do" list, expand-ahead browsing looks like a useful approach to build upon PygmyBrowse (see my live demo). The approach is described in "Expand-Ahead: A Space-Filling Strategy for Browsing Trees" by McGuffin et al. (doi:10.1109/INFOVIS.2004.21, PDF also here). There is a video on Ravin Balakrishnan's site, which is an AVI file that I haven't bee able to coerce my Mac into playing, hence I've posted it on YouTube.

Continuing the theme of viewing big trees, another approach to viewing large objects is tiling , which most people will have encountered if they've used Google Maps.The idea is to slice a large image into many smaller pieces ("tiles") at different reoslutions, and display only those tiles needed to show the view the user is interested in. I'd thought about doing this for trees but abandoned it. However, I think it is worth

I've refined my first efforts to now highlight where you are in the tree. The trees on display here now show the new look. Basically I've abandoned image maps as they don't allow me to highlight the part of the tree being selected. After some fussing I switched to using HTML DIVs, which sit on top of the image. This took a little while to get working, CSS and DIV placement drives me nuts.

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.

The PC hosting linnaeus.zoology.gla.ac.uk and darwin.zoology.gla.ac.uk has died, and this spells the end of my interest in (a) using generic PC hardware and (b) running Linux. The former keeps breaking down, the later is just harder than it needs to be (much as I like the idea). From now on, it's Macs only. No more geeky knapsacks for me. Because of this crash a lot of my experimental web sites are offline.

Well, the LSID discussion has just exploded in the last few weeks.