Overview

BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.

The project involves an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution.

The aim is to provide high performance evaluation ‘services’ to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This allows these packages to make use of implementations that make use of optimized hardware such as graphics processing units.

Currently the following software packages can make use of the BEAGLE library:

• BEAST
• BEAST2
• MrBayes

Support for BEAGLE is experimental or in development for the following packages:

• Garli
• PhyML
• RevBayes
• PAUP*

References

A manuscript describes the BEAGLE API and library: http://sysbio.oxfordjournals.org/content/61/1/170

The paper describing the algorithms used for calculating likelihoods of sequences on trees using many core devices like graphics processing units (GPUs) is available from: http://tree.bio.ed.ac.uk/publications/390/

Current binary installers

• BEAGLE v4.0.0 for macOS universal
• BEAGLE v4.0.0 for Windows 64-bit

Previous binary installers

• BEAGLE v3.1.0 for macOS with CUDA
• BEAGLE v3.1.0 for Windows 64-bit
• BEAGLE v2.1.2 for Mac OS X 10.6 and later
• BEAGLE v2.1.0 for Windows XP and later

Installation instructions

• Instructions for installing BEAGLE on macOS
• Instructions for installing BEAGLE on Windows
• Instructions for installing BEAGLE on Linux

Documentation

• Release notes
• API documentation
• Phylogenetic Software Development Tutorial

Code signing

• Free code signing provided by SignPath.io, certificate by SignPath Foundation. This program will not transfer any information to other networked systems unless specifically requested by the user or the person installing or operating it.

Acknowledgements

• This project is supported in part through the National Science Foundation grants IIS-1251151, DMS-1264153, DBI-1356562, DBI-1661443 & DEB-1354146; National Institutes of Health grants R01-HG006139, R01-AI107034, U19-AI135995 & R01-AI153044; Wellcome Trust grant 206298/Z/17/Z; and European Research Council grant 725422-ReservoirDOCS.