Between the Bodega Bay workshop and my spring semester class on computational phylogenetics at LSU, I’ve been talking a lot about phylogenetic analyses recently. In my opinion, one of the most underutilized approaches for summarizing phylogenetic information is to visualize collections of trees in tree space (or an approximation of tree space projected into 2 or 3 dimensions). These visualizations can help with diagnosing MCMC convergence problems, comparing the phylogenetic signal coming from different genes, picking an appropriate burn-in, and a whole bunch of other stuff. I widely recommend such visualizations to students. There are some drawbacks (e.g., lots of information can be lost during the projection to such low-dimensional spaces), but on balance it seems to me that the advantages outweigh these drawbacks. There really isn’t another way to summarize that amount of phylogenetic information in a single plot. As far as I know, the first paper to describe this approach was by Hillis, Heath, and St. John (2005, Syst. Biol., 54: 471-482), which included the release of a Mesquite plug-in called TreeSetViz for performing such visualizations using multi-dimensional scaling (MDS). I used this tool quite a lot and was disappointed that it became incompatible with newer releases of Mesquite. In fact, I maintained an outdated version of Mesquite just to run TreeSetViz. Well, unbeknownst to me, an updated version of TreeSetViz was released last year that is compatible with the most recent versions of Mesquite (hat tip to Vinson Doyle for pointing this out) and includes a wide variety of new options for comparing and visualizing trees. Strangely, this new release isn’t mentioned on the original TreeSetViz website, but it is announced, along with very simple installation instructions, on the Mesquite website. More recently, additional tools that are independent of Mesquite (TreeScaper) have been developed that also perform tree set visualization and projection. Give them a try!