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

Fourment Mathieu and Darling E. Aaron. Evaluating probabilistic programming and fast variational Bayesian inference in phylogenetics. doi:10.1101/702944.

Requirements

To reproduce the same results the exact version of the following programs should be used.

phylostan

physher vb-v1.0

beast v1.10.4

beast2 v2.5.2

The bwest package must be installed in order to use the Weibull distribution. phylostan uses the Weibull distribution to model rate heterogeneity across sites instead of the gamma distribution since automatic differentiation of the gamma distribution is not available in Stan.

The BEAST2 website has a blog post explaining how to install packages. This package is not part of the official package repository so you need to register this package first.

• Open BEAUTi, click on Manage Packages menu the in the File menu. This will open a window showing the package names.
• Click on the Package repositories button, then click on the Add URL button.
• Write the following url https://4ment.github.io/assets/beast2/packages.xml in the new window. Click Done to close the window.
• Locate and select the package name bwest in the table and click the Install/Upgrade button.
• Close the window et voila the package should be installed.

The executables phylostan, physher, beast, beast2 should be in the PATH.

Running the simulations

cd phylostan/examples
scons .

or using multithreading (5 threads in this case):

cd phylostan/examples
scons -j 5 .

The simulations will take several days to complete.

Generating the script files only

cd phylostan/examples
scons dry=1

To run physher on one the DS1 file:

cd examples/DS1/0
physher tree0.json