The latest version of the David and Wayne Maddison's Cartographer module for their program Mesquite can export KML files for Google Earth. They graciously acknowledge my crude efforts in this direction, and Bill Piel's work -- he really started this whole thing rolling.So, those of you inspired to try your hand at Google Earth trees, and who were frustrated by the lack of tools should grab a copy of Mesquite and take it for a spin.
Quick note to say how much fun it is to use Parallels Desktop. It's a great advantage to have Windows XP and Fedora Core 7 running on my Mac. As much as I dislike Internet Explorer, it caught some bugs in my code. It's always useful to try different environments when debugging code, either stand alone or for the Web.
Nature precedings is pre-publication server launched by Nature a few months ago. To quote from the website: Unable to resist, I've uploaded three manuscripts previously languishing as "Technical Reports" on my old server. The three I uploaded now have bright shiny DOIs, which may take a little while to register with CrossRef.
In an earlier post I described the TBMap database (doi:10.1186/1471-2105-8-158), which contains a mapping of TreeBASE taxon names onto names in other databases. While this is one step towards making it easier to query TreeBASE, what I'd really like is to link the data in TreeBASE to sources such as GenBank and specimen databases.
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