Co-estimation of phylogenetic and transmission trees in BEAST
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README.md

beastlier (BEAST Link Inference for Epidemiological Reconstruction)

This repository contains software for use with the method for transmission tree reconstruction in BEAST described in the paper:

Hall M, Woolhouse M, Rambaut A (2015) Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set. PLoS Comput Biol 11(12): e1004613. doi:10.1371/journal.pcbi.1004613

This repository is for a full BEAST 2 package which is currently under development. In addition, it contains two Python scripts:

  • A script (ModifyXML.py) that takes BEAST 1 XML output from BEAUTi (version 1.8.4 or later) and transforms it for transmission tree reconstruction. This will use lxml if it is installed, which is recommended as it produces nicer output, but will work without. Command line help is implemented (run the script with the -h argument).
  • A second script (MPCTree.py) to calculate the maximum parent credibility (MPC) transmission tree from the extra .net.txt file that ModifyXML.py makes BEAST produce (which logs the transmission tree).

Detailed documentation is available here.