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github.com/beast-dev/beast-mcmc @v10.5.0

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42,779 symbols 125,546 edges 3,436 files 6,897 documented · 16%

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README

BEAST X

BEAST X is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST X uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

Download BEAST X

Download BEAST v10.5 binaries for Mac, Windows and UNIX/Linux

Latest stable release Release Version Release Date Downloads

Latest development release Development Version Development Date Downloads

The previous major release of BEAST was v1.8.4 --- binaries for Mac, Windows and UNIX/Linux Downloads

Older BEAST Downloads

Other Downloads

BEASTGen v1.0.2 .tgz file

BEASTGen v1.0.2 .ZIP file

Documentation

BEAST Documentation Website

Development software

We use IntelliJ IDEA and java profiling via JProfile and YourKit

Acknowledgements

This work was supported in part by the European Union Seventh Framework Programme for research, technological development and demonstration under Grant Agreement no. 278433-PREDEMICS and no. 725422-ReservoirDOCS, the Wellcome Trust through collaborator award 206298/Z/17/Z, NSF grant DMS 1264153 and NIH grants R01 HG006139, R01 AI107034, U19 AI135995 and R01 AI153044.

Extension points exported contracts — how you extend this code

IValidatable (Interface)

@author Copyright (C) 2004 Grzegorz Kowal [14 implementers]

packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/IValidatable.java

SubstitutionModel (Interface)

model of sequence substitution (rate matrix) . provides a convenient interface for the computation of transition p [6 …

src/dr/oldevomodel/substmodel/SubstitutionModel.java

BeagleBasta (Interface)

(no doc) [3 implementers]

src/beagle/basta/BeagleBasta.java

Instance (Interface)

(no doc) [1 implementers]

src/test/dr/evomodel/treedatalikelihood/continuous/cdi/SafeMultivariateActualizedWithDriftIntegratorTest.java

Binding (Interface)

@author Copyright (C) 2005 Grzegorz Kowal [16 implementers]

packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Binding.java

SiteModel (Interface)

SiteModel - Specifies how rates and substitution models vary across sites. @author Andrew Rambaut @author Alexei Drummo [12 …

src/dr/oldevomodel/sitemodel/SiteModel.java

Instance (Interface)

(no doc) [1 implementers]

src/test/dr/inference/model/CompoundEigenMatrixTest.java

Describable (Interface)

(no doc) [3 implementers]

packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Describable.java

Core symbols most depended-on inside this repo

src/dr/xml/Report.java

packaging_tools/windows/launch4j/src/net/sf/launch4j/Log.java

src/dr/stats/Variate.java

src/dr/stats/Variate.java

getParameterValue

src/dr/inference/model/Parameter.java

src/dr/math/interfaces/PointSeries.java

src/dr/evomodel/alloppnet/speciation/AlloppNode.java

src/dr/app/checkpoint/BeastCheckpointer.java

Shape

Method 38,055

Class 4,059

Interface 327

Enum 219

Function 119

Languages

Java100%

C1%

Python1%

C++1%

Modules by API surface

src/dr/util/Transform.java394 symbols

src/dr/evomodel/arg/ARGModel.java250 symbols

src/dr/evomodel/tree/NewTreeModel.java123 symbols

src/dr/evomodel/bigfasttree/thorney/ConstrainedTreeModel.java121 symbols

src/dr/evomodel/alloppnet/speciation/MulSpeciesTreeModel.java120 symbols

src/dr/inference/operators/hmc/MassPreconditioner.java119 symbols

src/dr/evomodel/alloppnet/speciation/AlloppSpeciesNetworkModel.java116 symbols

src/dr/evomodel/speciation/SpeciesTreeModel.java115 symbols

src/dr/evolution/tree/TreeTrait.java113 symbols

src/dr/evomodel/tree/AncestralTraitTreeModel.java112 symbols

src/dr/evomodel/tree/DefaultTreeModel.java108 symbols

src/dr/evomodel/branchratemodel/ArbitraryBranchRates.java108 symbols

For agents

$ claude mcp add beast-mcmc \
  -- python -m otcore.mcp_server <graph>

⬇ download graph artifact