Skip to content
general purpose library for evaluating the likelihood of sequence evolution on trees
Branch: master
Clone or download
ayresdl modifications to empirical data set benchmarking; if custom topology …
…used with newtree option, then it is used in last replicate
Latest commit 2edfc40 Mar 5, 2019
Type Name Latest commit message Commit time
Failed to load latest commit information.
.travis updated .travis.yml, .travis/, m4/ax_openmp.m4 to same as m… Apr 19, 2018
java/beagle fix for BEAGLE pre-release version format Nov 5, 2018
libhmsbeagle add error # in case code is not recognized Feb 23, 2019
m4 updated .travis.yml, .travis/, m4/ax_openmp.m4 to same as m… Apr 19, 2018
project windows related fixes Nov 11, 2018
tests changed genomictest name to synthetictest; added additional options t… Apr 19, 2018
README Work in progress! Reorganizing codebase to conform to GNU library Jun 13, 2009
beagle-dox.png updated doxygen documentation and configuration file Oct 17, 2011
build.xml added options to synthetictest to read in alignment and tree files; a… Mar 1, 2019 fixed API version (should have stayed at 1 since API is backward comp… Nov 10, 2013


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:

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


A manuscript describes the BEAGLE API and library:

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:

Binary installers

Installation instructions



  • 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; Wellcome Trust grant 206298/Z/17/Z; and European Research Council grant 725422-ReservoirDOCS.
You can’t perform that action at this time.