phylorun 0.5.0

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🧬 PhyloRun

PhyloRun allows you to run BEAST X, BEAST 2, RevBayes, and LPhy experiments using a single tool.

📦 Installation

Use pip to install the CLI tool:

pip install --upgrade phylorun

🚀 Features

Run BEAST X, BEAST 2, RevBayes and LPhy analyses

phylorun someBeastXModel.xml
phylorun someBeast2Model.xml
phylorun someRevModel.rev
phylorun someRevModel.lphy

phylorun automatically detects which MCMC engine to use.

By default, phylorun tries to use your existing installation of the engine. If this fails, you can specify the location of the binary on your system:

phylorun --bin "/Applications/BEAST X 10.5.0/bin/beast" someBeastXModel.xml
phylorun --bin "/Applications/BEAST 2.7.7/bin/beast" someBeast2Model.xml
phylorun --bin "/usr/bin/rev" someRevModel.rev

If you don't have an engine installed on your local system, you can use the --container flag and phylorun automatically installs everything that's needed in an isolated environment:

phylorun --container someBeastXModel.xml
phylorun --container someBeast2Model.xml
phylorun --container someRevModel.rev

Currently, this does not work when your BEAST 2 analysis uses packages.

Run PhyloSpec analyses

phylorun can run a PhyloSpec analysis using any of the engines:

phylorun --beastx model.phylospec
phylorun --beast2 model.phylospec
phylorun --revbayes model.phylospec

Benchmark engines

You can use phylorun to see which engine is the fastest for your PhyloSpec model:

phylorun benchmark model.phylospec

Validate engines

You can use phylorun to validate that the engines produce the same results for your PhyloSpec model:

phylorun validate model.phylospec

Configuration

All unknown arguments are directly passed to the engine (put them at the end of the command):

phylorun someBeast2Model.xml -resume

For LPhy, arguments prefixed with --beast2 will be passed to BEAST 2 and not to LPhyBeast:

phylorun someLphyModel.lphy --beast2-resume