Bacter allows you to infer the ancestral recombination graph (ARG) that gave rise to your sampled data, including both clonal frame and the recombinant edges. Loci and sites affected by each conversion event are also inferred.
For informative data sets, Bacter can sample posterior distributions for parameters such as the recombination rate and expected converted tract length jointly with the ARG. For serially sampled data, joint estimation of the molecular clock rate is also possible.
Bacter includes support for producing Bayesian Skyline Plot (BSP) inferences of bacterial population dynamics. This inference may actually be more powerful when recombination is present in your data set.
Bacter is a package that extends the BEAST 2 computational phylogenetics system. Installation of the latest version (1.2.3) is via BEAST 2's built-in package manager and involves the following steps:
Congratulations, Bacter is now installed!
The documentation for Bacter can be found here. This documentation is still in development and thus does not comprehensively describe all features of Bacter, for instance treatment of Bayesian Skyline Plots. Documentation for these features will be be added soon.
If you use the Bacter package in research that leads to publication, please cite the following papers:
Bacter is maintained primarily by members of the Centre for Computational Evolution at the University of Auckland, New Zealand and mEpiLab at Massey University, New Zealand. Its development is generously supported by the following organizations: