Bayesian Evolutionary Analysis of Metastasis (BEAM)

BEAM is a BEAST2 package for Bayesian cancer migration graph inference from CRISPR cell lineage tracing data. BEAM provides a joint model of lineage reconstruction and migration history inference from the raw data, avoiding the need to condition on a single phylogeny while instead inferring a distribution of migration graphs.

Installation

1. Install BEAST2 from beast2.org
2. Install BEAGLE from beagle-dev.github.io
3. Install required BEAST2 packages based on xml declaration. The example uses the following:

   packagemanager -add BEAST_CLASSIC

4. Install BEAM:
   • Download the latest release from BEAM GitHub releases
   • Find your BEAST2 packages directory (check with packagemanager -list)
   • Create and set up BEAM in that directory (replacing vX.Y.Z with the latest version)

     mkdir beam && cd beam
     wget https://github.com/StephenStaklinski/beam/releases/download/vX.Y.Z/beam.vX.Y.Z.zip
     unzip beam.vX.Y.Z.zip

Verify installation by running packagemanager -list. Beam should appear in the list.

Usage

Basic Usage

Run BEAM using the BEAST2 command line interface:

beast -working examples/input.xml