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.
I have an "on again/off again" relationship with treemaps. Lately, I've been taking another look, partly inspired by Björn Engdahl's MSc thesis Ordered and Unordered Treemap Algorithms and Their Applications on Handheld Devices.
Greg Jordan and Bill Piel have released PhyloWidget, a Java applet for viewing phylogenetic trees. It's very slick, with some nice visual effects courtesy of Processing. PhyloWidget is open source, with code hosted by Google code. I'm a C++ luddite, so it took me a few moments to figure out how to build the applet, but it's simple enough, just type ant PhyloWidget at the command prompt.
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.
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.