19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology

This repository contains the pipeline and data sets supporting the results of the following article:

Fourment M, Magee A, Whidden C, Bilge A, Matsen IV FA, Minin VN. 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology. arXiv:1811.11804.

Requirements

physher

To reproduce the analysis the release marginal-v1.1 should be used and the executable should be located in the bin directory.

Running the simulations

cd marginal-experiments
python run_simulations.py

or using Docker (no need to install physher)

cd marginal-experiments
docker pull 4ment/marginal-experiments
docker run -v $PWD:/data 4ment/marginal-experiments

The simulations will take several weeks to complete. Multiple directories will be produced (DS1, DS2, DS3, DS4, DS5).

Parsing results

Rscript -e 'rmarkdown::render("DS.Rmd")'

The script will generate the file DS.pdf.