Parker J, Rambaut A, Pybus OG (2008) Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infection, Genetics & Evolution 8:239-46

Author: Joe Parker

Download program:

Download manual: BaTSmanual.pdf

Download teaching slides: BaTSslides.ppt


Phylogeny-trait association is defined as the extent to which neighbouring taxa in a phylogenetic tree share a character of interest. This may be a classical phenotypic trait, a molecular attribute, disease progression type, geographic location or any other character that can be coded as a set of discrete states with equal weighting. BaTS is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.

A new version of BaTS is being developed and tested, see here.


To run BaTS, you will need Java 1.5.0 (J2SE 5.0) or higher; see included documentation for more details. The download contains an executable jar file that will run on PC, Mac, UNIX and LINUX operating systems.