├── .gitignore ├── LICENSE.md ├── README.md ├── bin └── examples │ └── validation │ ├── README.md │ ├── gene.nodes.3taxon.png │ ├── gene.nodes.4taxon.png │ ├── gene.topologies.3taxon.png │ ├── gene.topologies.4taxon.png │ ├── plot_comparisons.R │ ├── prior_sampling_nonstarbeast │ ├── nonstarbeast_3taxon.xml │ ├── nonstarbeast_3taxon_fixedSpeciesTree.xml │ └── nonstarbeast_4taxon.xml │ ├── prior_sampling_starbeast │ ├── computeGeneTreeTopologyDist.xml │ ├── computeSpeciesTreeTopologyDist.xml │ ├── starbeast_3taxon.xml │ └── starbeast_4taxon.xml │ ├── run_analyses.sh │ ├── species.nodes.3taxon.png │ ├── species.nodes.4taxon.png │ ├── species.topologies.3taxon.png │ └── species.topologies.4taxon.png ├── fxtemplates ├── AIM.xml ├── SpeciesTreeRLC.xml ├── SpeciesTreeUCED.xml ├── SpeciesTreeUCLN.xml ├── StarBeast2.xml ├── sbClockModels.xml ├── sbPopModels.xml ├── sbSubstModels.xml └── sbTreePriors.xml ├── lib ├── COPYING └── guava-23.0.jar ├── src ├── sb2tests │ ├── BigCoordinatedExchangeTest.java │ ├── ConstantIOTest.java │ ├── ConstantPopulationTest.java │ ├── ExchangeTestHelper.java │ ├── IncompatibleTreeTest.java │ ├── LinearWithConstantRootTest.java │ ├── MissingDataConstantIOTest.java │ ├── MissingDataCoordinatedExchangeTest.java │ ├── SmallCoordinatedExchangeTest.java │ ├── StarbeastClockTest.java │ ├── TreeLengthLoggerTest.java │ ├── UncorrelatedRatesTest.java │ └── WideExchangeTest.java └── starbeast2 │ ├── AdaptiveOperator.java │ ├── AllEqual.java │ ├── ConstantPopulations.java │ ├── ConstantWithGeneFlow.java │ ├── CoordinatedExchange.java │ ├── CoordinatedExponential.java │ ├── CoordinatedOperator.java │ ├── CoordinatedUniform.java │ ├── DiscreteRateCycle.java │ ├── DiscreteRateUniform.java │ ├── DummyModel.java │ ├── Euler2ndOrderAIM.java │ ├── GeneTree.java │ ├── GeneTreeWithMigration.java │ ├── LinearWithConstantRoot.java │ ├── MaximumDouble.java │ ├── MigrationModel.java │ ├── MinimalBranchLength.java │ ├── MinimumDouble.java │ ├── MultispeciesCoalescent.java │ ├── NetworkRateExchange.java │ ├── NodeHeightComparator.java │ ├── NodeReheight2.java │ ├── Overlap.java │ ├── PassthroughModel.java │ ├── PopulationModel.java │ ├── RandomLocalRates.java │ ├── RealCycle.java │ ├── SAMau1999.java │ ├── STDirectionalLogger.java │ ├── SanityChecks.java │ ├── SpeciesTree.java │ ├── SpeciesTreeInterface.java │ ├── SpeciesTreeLogger.java │ ├── SpeciesTreeLoggerWithGeneFlow.java │ ├── SpeciesTreeParser.java │ ├── SpeciesTreeRates.java │ ├── StarBeastClock.java │ ├── StarBeastInitializer.java │ ├── StarBeastTaxonSet.java │ ├── TreeLengthLogger.java │ ├── TreeStats.java │ ├── UncorrelatedRates.java │ ├── UniformPopulations.java │ ├── aimannotator │ ├── AIMannotator.java │ ├── RankedCladeSystem.java │ └── UnrankedCladeSystem.java │ ├── aimoperator │ ├── ExchangeAndSwap.java │ ├── RankingAwareOperator.java │ ├── SubtreeSlideAndSwap.java │ ├── UniformAndSwap.java │ └── WilsonBaldingAndSwap.java │ ├── app │ └── beauti │ │ ├── StarBeastAlignmentProvider.java │ │ ├── StarBeastMorphModelAlignmentProvider.java │ │ └── StarBeastTipDatesInputEditor.java │ ├── math │ └── distributions │ │ └── AltInverseGamma.java │ └── utils │ ├── BernoulliDistribution.java │ ├── GeneTreeSimulator.java │ ├── NodeHeightLogger.java │ ├── SimulatedGeneTree.java │ ├── SimulatedGeneTreeLogger.java │ ├── TreeTopologyDistGenerator.java │ ├── TreeTopologyDistLogger.java │ └── TreeTraceAnalysisWithError.java ├── tutorial ├── CanisFBD │ └── Canis-FBD.xml ├── CanisPhylogeny │ └── Canis-Phylogeny.xml ├── CanisUCLN │ └── Canis-UCLN.xml ├── StarBEAST2-refs.bib ├── StarBEAST2-tutorial.tex ├── data │ ├── APOBS1.fasta │ ├── APOBS2.fasta │ ├── BDNF.fasta │ ├── BRCA1S1.fasta │ ├── BRCA1S2.fasta │ ├── CHST12.fasta │ ├── CMKOR1.fasta │ ├── Ch14.fasta │ ├── Ch21.fasta │ ├── Ch24.fasta │ ├── FGFR3.fasta │ ├── GHRex09.fasta │ ├── RAG1.fasta │ ├── TMEM20.fasta │ ├── VANGL2.fasta │ ├── VWF.fasta │ ├── morphology_canis.nex │ └── tip_dates_canis.dat └── figures │ ├── addMorphology.png │ ├── birthDeathModel.png │ ├── chainLength.png │ ├── changeTreePrior.png │ ├── clockPriors.png │ ├── clockRateHistogram.png │ ├── clockRateTrace.png │ ├── cloneSiteModel.png │ ├── constantPopulations.png │ ├── densitree.png │ ├── estimateMorphClock.png │ ├── fastaFileImport.png │ ├── guessTaxonMap.png │ ├── hky.png │ ├── icytree.png │ ├── installStarBEAST2.png │ ├── linkModels.png │ ├── managePackages.png │ ├── morphologyPartitions.png │ ├── sampledAncestorsDensitree.png │ ├── sampledAncestorsIcyTree.png │ ├── samplingRate.png │ ├── speciesTreeUCLN.png │ ├── strictClockModel.png │ ├── strictClockTemplate.png │ ├── taxonMap.png │ ├── tipDates.png │ ├── tracerPosterior.png │ ├── tracerUCLN.png │ ├── treeAnnotator.png │ ├── treeAnnotatorMeanHeights.png │ └── uclnClockRates.png └── version.xml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/genomescale/starbeast2/HEAD/.gitignore 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