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BEAST phylonco

This is a BEAST2 package for Bayesian inference of molecular data for cancer evolution. This package implements error models and substitution models for inference of timed trees in a Bayesian MCMC framework.

Paper: Chen, K., Moravec, J. C., Gavryushkin, A., Welch, D., & Drummond, A. J. (2022). Accounting for errors in data improves divergence time estimates in single-cell cancer evolution. Molecular biology and evolution, 39(8), msac143.

See bioDS/beast-phylonco-paper for datasets and analyses in the paper.

Software requirements

This package requires Java 8, and at least

See dependencies in version.xml

Features

The current release has the following features.

Error Models

  • GT16 diploid nucleotide error model (16 states)
  • Binary error model
  • Nucleotide error model (4 states - A, G, C, T)
  • General error model (n states)

Substitution Models

  • GT16 diploid nucleotide model (16 states)
  • Binary substitution model
  • SiFit2 substitution model (2 states)
  • SiFit3 substitution model (3 states)

User guide

How to install

You may install the Phylonco package using the Package Manager.

Start BEAUti, open the Package Manager by selecting File -> Manage packages from the Menu.

Click Package repositories to open a new popup window

Click Add URL and add "https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra.xml" to the entry.

Click Done. The Phylonco package should now appear in the Package Manager

From the Package Manager, select Phylonco and click Install/Upgrade to install.

Input format

All models accept input genotypes in FASTA and Nexus formats. See here for the genotype codes.

For the GT16 model, VCF files can be converted to FASTA format using www.github.com/bioDS/vcf2fasta

Running BEAST

Start the BEAST software

Make sure the "Use BEAGLE library" box is unchecked

Set the input file to one of the examples e.g., examples/test_GT16_error.xml

Running BEAST on command line

Launch beast in java only mode by adding the -java option, e.g.

Windows
java -jar c:\Users\BEASTUser\Desktop\BEAST\lib\launcher.jar -java beast.xml

Mac
/Applications/BEAST\ 2.6.6/bin/beast -java beast.xml

Linux
~/beast/bin/beast -java beast.xml

How to run BEAUti

BEAUti UI is currently only supported for the Binary Substitution model. We are currently working on this :)

Tutorials and new models will be added once Beauti support is completed.

For developers

To build use ./gradlew clean build in the root directory, for details see dev notes

For manual package installation instructions, see here

Citations