Bacterial phylogenetics in BEAST 2
Bacter is a BEAST 2 package which facilitates joint Bayesian inference of ancestral recombination graphs (ARG) and related parameters from bacterial sequence alignments under the ClonalOrigin model.
Use Bacter to infer...
ARGs
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.
Parameters
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.
Population dynamics
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.
Installation
Bacter is a package that extends the BEAST 2 computational phylogenetics system. Installation of the latest version (3.0.1) is via BEAST 2's built-in package manager and involves the following steps:
- Download an install the latest version of BEAST 2 from the project's web page at www.beast2.org.
- Open the BEAUti program.
- From the File menu select "Manage Packages".
- Locate Bacter in the list and select it.
- Press the Install/Upgrade button.
Congratulations, Bacter is now installed!
Documentation
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.
Citing Bacter
If you use the Bacter package in research that leads to publication, please cite the following papers:
- T. G. Vaughan, D. Welch, A. J. Drummond, P. J. Biggs, T. George, N. P. French,
Inferring Ancestral Recombination Graphs from Bacterial Genomic Data,
GENETICS February 1, 2017 vol. 205 no. 2, 857-870; DOI: 10.1534/genetics.116.193425 - X. Didelot, D. Lawson, A. Darling, D. Falush,
Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences, GENETICS December 1, 2010 vol. 186 no. 4, 1435-1449; DOI: 10.1534/genetics.110.120121
Acknowledgements
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:
