Thursday, May 15, 2008

Are We There Yet? - Redux

A few weeks ago I wrote about my frustration with learning about the program Are We There Yet (AWTY), which was designed to help diagnose convergence in Bayesian phylogenetic analyses. Now, with some help from Dan Warren (one of the packages developers), I'm starting to figure it out. It's a diamond in the rough, valuable not only for diagnosing convergence, but also for visualizing similarity among alternative tree topologies and support values (I was tipped off to the later use by McGuire et al.'s recent Sys. Bio. paper on hummingbirds). Check out the figures generated using the "Compare" feature. This figure compares posterior probability values for each node in two samples of trees (the axes range from 0-100 and represent posterior probabilities). Nodes that have the same posterior probability in both sets of trees will fall along the diagonal. Nodes whose posterior probabilities differ between the two samples will fall of this diagonal. AWTY can also identify topological incongruence: if a node is present in one tree and absent in the other it will have a 0 along one axis.

The figure on the left is from two independent analyses that used the same data and partitioning strategy. The relatively tight fit of this data to the diagonal indicates similarity of support values and topologies between these two samples. The figure on the right is from analyses run using different partitioning strategies. Although the scatter is somewhat higher, most nodes whose support differs between the samples are relatively poorly supported in both. Moreover, there are no nodes with posteriors of >20 in one sample that are absent from the other, indicating topological concordance.

Good stuff. Now I just need to figure out how to get around the restrictive web interface...

1 comment:

Glor said...

An informative presentation about AWTY and its application to questions about convergence can be found at: ""