The Phylo Lab works on evolutionary history methodology and algorithms in Biology and Historical Linguistics. Recent work by the group has focused on five major issues, all related to evolutionary history reconstruction:

• New algorithms for simultaneous reconstruction of a phylogeny and multiple sequence alignment (see this page for some discussion about our approach).
• Fast techniques for NP-hard optimization problems, such as maximum likelihood and maximum parsimony. Our research has produced a very powerful technique called "Rec-I-DCM3" for dramatically speeding up even the best of the current heuristics for maximum parsimony and maximum likelihood on large datasets. This software is part of the CIPRES project, and can be used in the CIPRES portal for large dataset analyses.
• The inference of complex evolutionary histories. In this area, I have focused on the inference of evolution from whole genomes, and the detection and inference of reticulate evolution (i.e., horizontal gene transfer and/or hybridizing speciation).
• The analytical study of convergence rates of different methods, and the development of provably fast converging methods.
• Computational phylogenetics in historical linguistics (see also this write-up at NSF, and this page). (On March 21, 2005, Harvard University sponsored a workshop on this topic, which Tandy Warnow and Jay Jasanoff (Chair of the Linguistics Department at Harvard University) co-organized; see this page for more information, and click here for a poster of the workshop.)