Documentation Overview

Bacter is a BEAST 2 package dedicated to performing inference of bacterial sequence data. In general, it allows for joint inference of the Ancestral Recombination Graph (ARG), recombination rates, tract lengths, substitution rate and population dynamics. Exactly what may be inferred from a given data set depends heavily on the size of the data set, and the rates of recombination and mutation for the population under study, and the sampling procedure.

The documentation for Bacter currently consists of:

1. the installation instructions, and
2. a basic tutorial.

Please complete the tutorial before attempting to analyze your own data.