walterxie
commented
6 years ago Find installed and available 35 packages. ====== Package 1 : BEAST ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BEAST/lib/beast.jar
beast.core.MCMC Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results.
beast.evolution.branchratemodel.UCRelaxedClockModel Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biol 4(5): e88 10.1371/journal.pbio.0040088
Description : Defines an uncorrelated relaxed molecular clock.
beast.evolution.speciation.BirthDeathGernhard08Model Gernhard 2008. The conditioned reconstructed process. Journal of Theoretical Biology Volume 253, Issue 4, 21 August 2008, Pages 769-778 doi:10.1016/j.jtbi.2008.04.005
Description : Birth Death model based on Gernhard 2008.
This derivation conditions directly on fixed N taxa.
The inference is directly on b-d (strictly positive) and d/b (constrained in [0,1))
Verified using simulated trees generated by Klass tree sample. (http://www.klaashartmann.com/treesample/)
Sampling proportion not verified via simulation. Proportion set by default to 1, an assignment which makes the expressions identical to the expressions before the change.
beast.evolution.speciation.CalibratedYuleModel Heled J, Drummond AJ (2012) Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation. Systematic Biology 61(1):138-149. 10.1093/sysbio/syr087
Description : Yule prior with calibrated monophyletic clades. With this prior, the marginal distribution of the calibrated nodes (the MRCA of clades) is identical to the specified calibration, but the Yule is not preserved over the whole tree space, only among sub-spaces.
beast.evolution.substitutionmodel.HKY Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174. 10.1007/BF02101694
Description : HKY85 (Hasegawa, Kishino & Yano, 1985) substitution model of nucleotide evolution.
beast.evolution.substitutionmodel.TN93 Tamura, K., & Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10(3), 512-526.
Description : TN93 (Tamura and Nei, 1993) substitution model of nucleotide evolution.
Find total 6 cited BEAST classes.
====== Package 2 : bacter ======
Load classes from : ~/Library/Application Support/BEAST/2.5/bacter/lib/bacter.v2.1.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/bacter/lib/feast.v5.0.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/bacter/lib/guava-17.0.jar
bacter.ConversionGraph TG Vaughan, D Welch, AJ Drummond, PJ Biggs, T George, NP French Inferring Ancestral Recombination Graphs from Bacterial Genomic Data, Genetics, 205(2):857 (2017)
Description : Conversion graph based around the clonal frame.
bacter.devutils.MCMCTrace Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : An extension of MCMC that generates a detailed trace of the chain, including operators used, states proposed, Hastings ratios and acceptance probabilities.
bacter.model.SimulatedACG TG Vaughan, D Welch, AJ Drummond, PJ Biggs, T George, NP French Inferring Ancestral Recombination Graphs from Bacterial Genomic Data, Genetics, 205(2):857 (2017)
Description : Simulates an ARG under the full ClonalOrigin model - can be used for chain initialization or for sampler validation.
Find total 3 cited BEAST classes.
====== Package 3 : BADTRIP ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BADTRIP/lib/BADTRIP.v1.0.0.jar
beast.evolution.substitutionmodel.PoMoGeneral De Maio, Schloetterer and Kosiol (2013). Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Molecular Biology and Evolution 30(10), 2249-2262.
De Maio, Schrempf and Kosiol (2015). PoMo: An Allele Frequency-Based Approach for Species Tree Estimation. Systematic Biology doi: 10.1093/sysbio/syv048.
Description : Specifies transition probability matrix for PoMo. Not in general reversible, unless fitnesses are equal and root frequencies are not estimated.
Find total 1 cited BEAST classes.
====== Package 4 : BASTA ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BASTA/lib/BASTA.v3.0.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BASTA/lib/guava-15.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BASTA/lib/jblas-1.2.3.jar
multitypetreeVolz.distributions.PureStructuredCoalescentTreeDensityVolz New Routes to Phylogeography. De Maio N., Wu C., O'Reilly K., Wilson D. 2015, PLOS Genetics
Description : Not documented!!!
multitypetreeVolz.distributions.StructuredCoalescentTreeDensityVolz New Routes to Phylogeography. De Maio N., Wu C., O'Reilly K., Wilson D. 2015, PLOS Genetics
Description : Likelihood of Coalescent tree (Volz-type) under the Volz approximation to the structured coalescent.
Find total 2 cited BEAST classes.
====== Package 5 : MultiTypeTree ======
Load classes from : ~/Library/Application Support/BEAST/2.5/MultiTypeTree/lib/guava-15.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/MultiTypeTree/lib/jblas-1.2.3.jar Load classes from : ~/Library/Application Support/BEAST/2.5/MultiTypeTree/lib/MultiTypeTree.v7.0.0.jar
beast.evolution.tree.MultiTypeTree Timothy G. Vaughan, Denise Kuhnert, Alex Popinga, David Welch and Alexei J. Drummond, 'Efficient Bayesian inference under the structured coalescent', Bioinformatics 30:2272, 2014.
Description : A multi-type phylogenetic tree.
beast.evolution.tree.MultiTypeTreeFromFlatTree Timothy G. Vaughan, Denise Kuhnert, Alex Popinga, David Welch and Alexei J. Drummond, 'Efficient Bayesian inference under the structured coalescent', Bioinformatics 30:2272, 2014.
Description : Class to initialise a MultiTypeTree from a BEAST tree in which single-child nodes represent type changes.
beast.evolution.tree.MultiTypeTreeFromNewick Timothy G. Vaughan, Denise Kuhnert, Alex Popinga, David Welch and Alexei J. Drummond, 'Efficient Bayesian inference under the structured coalescent', Bioinformatics 30:2272, 2014.
Description : Class to initialize a MultiTypeTree from single child newick tree with type metadata
beast.evolution.tree.MultiTypeTreeFromUntypedNewick Timothy G. Vaughan, Denise Kuhnert, Alex Popinga, David Welch and Alexei J. Drummond, 'Efficient Bayesian inference under the structured coalescent', Bioinformatics 30:2272, 2014.
Description : Class to initialize a MultiTypeTree from single child newick tree with type metadata
beast.evolution.tree.RandomMultiTypeTree Timothy G. Vaughan, Denise Kuhnert, Alex Popinga, David Welch and Alexei J. Drummond, 'Efficient Bayesian inference under the structured coalescent', Bioinformatics 30:2272, 2014.
Description : Class to initialize a MultiTypeTree from random tree by adding minimum number of changes needed
beast.evolution.tree.StructuredCoalescentMultiTypeTree Timothy G. Vaughan, Denise Kuhnert, Alex Popinga, David Welch and Alexei J. Drummond, 'Efficient Bayesian inference under the structured coalescent', Bioinformatics 30:2272, 2014.
Description : A multi-type tree generated randomly from leaf types anda migration matrix with fixed population sizes.
multitypetree.operators.BeerliFelsenstein Beerli and Felsenstein, Genetics 152:763 (1999).
Description : Joint migration/tree operator described by Beerliand Felsenstein, Genetics, 1999.
Find total 7 cited BEAST classes.
====== Package 6 : BDMM ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BDMM/lib/BDMM.addon.jar
beast.evolution.speciation.BirthDeathMigrationClusterModelUncoloured Kuehnert D, Stadler T, Vaughan TG, Drummond AJ. 2016. Phylodynamics with migration: A computational framework to quantify population structure from genomic data. Mol Biol Evol. 33(8):2102–2116.
Description : UNTESTED! Birth-Death-Migration-model that allows distribution over parameters shared by clusters
beast.evolution.speciation.BirthDeathMigrationModel Kuehnert D, Stadler T, Vaughan TG, Drummond AJ. 2016. Phylodynamics with migration: A computational framework to quantify population structure from genomic data. Mol Biol Evol. 33(8):2102–2116.
Description : This model implements a multi-deme version of the BirthDeathSkylineModel with discrete locations and migration events among demes. This should only be used when the migration process along the phylogeny is important. Otherwise the computationally less intense BirthDeathMigrationModelUncoloured can be employed.Two implementations are available. The first is the fast classic one; the second one prevents underflowing, using so-called 'SmallNumbers', with the cost of additional computational complexity
beast.evolution.speciation.BirthDeathMigrationModelUncoloured Kuehnert D, Stadler T, Vaughan TG, Drummond AJ. 2016. Phylodynamics with migration: A computational framework to quantify population structure from genomic data. Mol Biol Evol. 33(8):2102–2116.
Description : This model implements a multi-deme version of the BirthDeathSkylineModel with discrete locations and migration events among demes. This should be used when the migration process along the phylogeny is irrelevant. Otherwise the BirthDeathMigrationModel can be employed.This implementation also works with sampled ancestor trees.Two implementations are available. The first is the fast classic one; the second one prevents underflowing, using so-called 'SmallNumbers', with the cost of additional computational complexity
beast.evolution.speciation.PiecewiseBirthDeathMigrationDistribution Kuehnert D, Stadler T, Vaughan TG, Drummond AJ. 2016. Phylodynamics with migration: A computational framework to quantify population structure from genomic data. Mol Biol Evol. 33(8):2102–2116.
Description : Piece-wise constant rates are assumed to be ordered by state and time. First k entries of an array give values belonging to type 1, for intervals 1 to k, second k intervals for type 2 etc.
beast.evolution.tree.InitialMultiTypeTreeFromMaster Timothy G. Vaughan, Denise Kuhnert, Alex Popinga, David Welch and Alexei J. Drummond, 'Efficient Bayesian inference under the structured coalescent', Bioinformatics 30:2272, 2014.
Description : Make a MultiTypeTree with tip dates and states obtained from MASTER simulation
Find total 5 cited BEAST classes.
====== Package 7 : BDSKY ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BDSKY/lib/BDSSM.addon.jar
beast.evolution.speciation.BirthDeathSkylineDiversifiedSampling Zhang C., Stadler T., Klopfstein S., Heath T.A., Ronquist F. 2016. Total-evidence dating under the fossilized birth-death process. Syst. Biol. 65:228–249. See also: Stadler T., Smrckova J. 2016. Estimating shifts in diversification rates based on higher-level phylogenies. Biol. Lett. 12:20160273.
Description : Extension of the birth-death skyline model to account for diversified sampling of extant taxa.
beast.evolution.speciation.BirthDeathSkylineModel Stadler, T., Kuehnert, D., Bonhoeffer, S., and Drummond, A. J. (2013): Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). PNAS 110(1): 228–33. If sampled ancestors are used then please also cite: Gavryushkina A, Welch D, Stadler T, Drummond AJ (2014) Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol 10(12): e1003919. doi:10.1371/journal.pcbi.1003919
Description : Adaptation of Tanja Stadler's BirthDeathSamplingModel, to allow for birth and death rates to change at times t_i
Find total 2 cited BEAST classes.
====== Package 8 : BEASTLabs ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTLabs/lib/BEASTlabs.addon.jar
beast.core.MCMC2 A prototype for BEAST 2.0: The computational science of evolutionary software. Bouckaert, Drummond, Rambaut, Alekseyenko, Suchard & the BEAST Core Development Team. 2010
Description : MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results.
beast.evolution.substitutionmodel.ComplexSubstitutionModel Edwards, Ceiridwen J., et al. Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology 21.15 (2011): 1251-1258.
Description : Complex-diagonalizable, irreversible substitution model
beast.evolution.substitutionmodel.LazyHKY Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22:160-174. 10.1007/BF02101694
Description : Lazy version of HKY85 substitution model of nucleotide evolution.
beast.inference.HeatedMCMC Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : Base class for doing Metropolis coupled MCMC. Each instance represenst a chain at a different temperature.
beast.inference.MCMCMC Altekar G, Dwarkadas S, Huelsenbeck J and Ronquist F (2004). Parallel Metropolis Coupled Markov Chain Monte Carlo For Bayesian Phylogenetic Inference. Bioinformatics, 20(3), 407-415. 10.1093/bioinformatics/btg427
Description : Metropolis-Coupled Markov Chain Monte CarloNote that log file names should have $(seed) in their name so that the first chain uses the actual seed in the file name and all subsequent chains add one to it.Furthermore, the log and tree log should have the same sample frequency.
beast.inference.MCMCParticle Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : MCMC chain that synchronises through files. Can be used with ParticleFilter instead of plain MCMC.
beast.inference.MCMCParticleAsync Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : MCMC chain to be launched by ParticleFilter. It updates its state without synchronisation with any of the other particles.
beast.inference.ML Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : Maximum likelihood throught simple random hill climbing
beast.inference.MultiMCMC Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : Runs multiple MCMC chains in parallel and reports Rubin-Gelman statistic while running the chain for each item in the first log file as well as the maximum difference in clade probability for every pair of chains. Note that log file names should have $(seed) in their name so that the first chain uses the actual seed in the file name and all subsequent chains add one to it.Furthermore, the log and tree log should have the same sample frequency.
beast.inference.SimulatedAnnealing Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : Maximum likelihood by simulated annealing
Find total 10 cited BEAST classes.
====== Package 9 : BEAST_CLASSIC ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEAST_CLASSIC/lib/mtj.jar
beast.evolution.substitutionmodel.LG Le, S. Q. and O. Gascuel. 2008. Mol. Biol. Evol. 25(7):1307-1320.
Description : LG model of amino acid evolution (Le and Gascuel, 2008)
beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel Edwards, Ceiridwen J., et al. Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology 21.15 (2011): 1251-1258.
Description : SVS General Substitution Model
beast.evolution.tree.coalescent.GMRFMultilocusSkyrideLikelihood Minin, Bloomquist and Suchard (2008) Molecular Biology and Evolution, 25, 1459-1471
Description : ...
beast.evolution.tree.coalescent.GMRFSkyrideLikelihood Minin, Bloomquist and Suchard (2008) Molecular Biology and Evolution, 25, 1459-1471
Description : A likelihood function for a Gaussian Markov random field on a log population size trajectory
Find total 4 cited BEAST classes.
====== Package 10 : BEASTShell ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTShell/lib/autocomplete.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTShell/lib/BEASTShell.addon.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTShell/lib/itextpdf-5.2.1.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTShell/lib/jtikz.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTShell/lib/rsyntaxtextarea.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTShell/lib/xchart-2.3.3-SNAPSHOT.jar
Find total 0 cited BEAST classes.
====== Package 11 : BEASTvntr ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTvntr/lib/BEASTvntr.addon.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTvntr/lib/EJML-core-0.29.jar Load classes from : ~/Library/Application Support/BEAST/2.5/BEASTvntr/lib/EJML-dense64-0.29.jar
beast.evolution.substitutionmodel.Sainudiin Raazesh Sainudiin et al. (2004) Microsatellite Mutation Models. Genetics 168:383-395 Chieh-Hsi Wu and Alexei J. Drummond. (2011) Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo. Genetics 188:151-164 10.1534/genetics.103.022665
Description : Substitution model of Sainudiin (R. Sainudiin et al., 2004) using Wu's modification (C. Wu and A.J. Drummond, 2011) for VNTR evolution.
beast.evolution.substitutionmodel.SainudiinComputedFrequencies Raazesh Sainudiin et al. (2004) Microsatellite Mutation Models. Genetics 168:383-395 Chieh-Hsi Wu and Alexei J. Drummond. (2011) Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo. Genetics 188:151-164 10.1534/genetics.103.022665
Description : Substitution model of Sainudiin (R. Sainudiin et al., 2004) using Wu's modification (C. Wu and A.J. Drummond, 2011) for VNTR evolution, where the frequencies of the root node are computed from the model.
beast.evolution.substitutionmodel.SainudiinComputedFrequenciesVanilla Raazesh Sainudiin et al. (2004) Microsatellite Mutation Models. Genetics 168:383-395 Chieh-Hsi Wu and Alexei J. Drummond. (2011) Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo. Genetics 188:151-164 10.1534/genetics.103.022665
Description : Substitution model of Sainudiin (R. Sainudiin et al., 2004) using Wu's modification (C. Wu and A.J. Drummond, 2011) for VNTR evolution, where the frequencies of the root node are computed from the model.
beast.evolution.substitutionmodel.SainudiinVanilla Raazesh Sainudiin et al. (2004) Microsatellite Mutation Models. Genetics 168:383-395 Chieh-Hsi Wu and Alexei J. Drummond. (2011) Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo. Genetics 188:151-164 10.1534/genetics.103.022665
Description : Substitution model of Sainudiin (R. Sainudiin et al., 2004) using Wu's modification (C. Wu and A.J. Drummond, 2011) for VNTR evolution.
Find total 4 cited BEAST classes.
====== Package 12 : bModelTest ======
Load classes from : ~/Library/Application Support/BEAST/2.5/bModelTest/lib/bModelTest.addon.jar
beast.evolution.sitemodel.BEASTModelTest Remco Bouckaert. bModelTest: Bayesian site model selection for nucleotide data. BioRxiv 2015/06/11/020792 http://dx.doi.org/10.1101/020792
Description : Used for backward compatibiliy only, so files generated with previous versions of modeltest can still run:
beast.evolution.sitemodel.BEASTModelTestSiteModel Remco Bouckaert. bModelTest: Bayesian site model selection for nucleotide data. BioRxiv 2015/06/11/020792 http://dx.doi.org/10.1101/020792
Description : Site model that jumps between with and without gamma sites, as well as with and without invariant sites
Find total 2 cited BEAST classes.
====== Package 13 : GEO_SPHERE ======
Load classes from : ~/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/GEO.addon.jar Load classes from : ~/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/Jama-1.0.1.jar Load classes from : ~/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jdom.jar Load classes from : ~/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jts-1.8.jar Load classes from : ~/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jump-core-1.2.jar Load classes from : ~/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/jump-workbench-1.2.jar Load classes from : ~/Library/Application Support/BEAST/2.5/GEO_SPHERE/lib/xerces.jar
sphericalGeo.ApproxMultivariateTraitLikelihood Remco R. Bouckaert. Phylogeography by diffusion on a sphere: whole world phylogeography. 2016, PeerJ 4:e2406 https://doi.org/10.7717/peerj.2406 10.7717/peerj.2406
Description : Approximate likelihood by MAP approximation of internal states
sphericalGeo.ApproxMultivariateTraitLikelihood2 Remco R. Bouckaert. Phylogeography by diffusion on a sphere: whole world phylogeography. 2016, PeerJ 4:e2406 https://doi.org/10.7717/peerj.2406 10.7717/peerj.2406
Description : Approximate likelihood by MAP approximation of internal states optimised to take sampled nodes in account
sphericalGeo.ApproxMultivariateTraitLikelihoodF Remco R. Bouckaert. Phylogeography by diffusion on a sphere: whole world phylogeography. 2016, PeerJ 4:e2406 https://doi.org/10.7717/peerj.2406 10.7717/peerj.2406
Description : Approximate likelihood by MAP approximation of internal states
sphericalGeo.ApproxMultivariateTraitLikelihoodF2 Remco R. Bouckaert. Phylogeography by diffusion on a sphere: whole world phylogeography. 2016, PeerJ 4:e2406 https://doi.org/10.7717/peerj.2406 10.7717/peerj.2406
Description : Approximate likelihood by MAP approximation of internal states optimised to take sampled nodes in account. Efficiently calculates geo priors as well.
Find total 4 cited BEAST classes.
====== Package 14 : BREAK_AWAY ======
Load classes from : ~/Library/Application Support/BEAST/2.5/BREAK_AWAY/lib/BREAK_AWAY.addon.jar
beast.geo.SampledTraitLikelihood Remco R. Bouckaert, Claire Bowern, Quentin D. Atkinson. The origin and expansion of Pama-Nyungan languages across Australia. Nature Ecology and Evolution, 2, 741–749 (2018) doi:10.1038/s41559-018-0489-3
Description : Treelikelihood that provides positions and calculates likelihood based on a graph based substitution model
Find total 1 cited BEAST classes.
====== Package 15 : CA ======
Load classes from : ~/Library/Application Support/BEAST/2.5/CA/lib/CA.addon.jar
beast.math.distributions.FossilPrior Michael Matschiner and Remco Bouckaert. A rough guide to CladeAge, 2013
Description : Prior based on information from the fossil record
Find total 1 cited BEAST classes.
====== Package 16 : CodonSubstModels ======
Load classes from : ~/Library/Application Support/BEAST/2.5/CodonSubstModels/lib/CodonSubstModels.v1.1.0.jar
codonmodels.CodonFrequencies Yang, Z. (2006). Computational molecular evolution. Oxford University Press.
Description : The equilibrium codon frequencies PI, including equal, F1X4, F3X4, and F60/F61.
codonmodels.M0Model Goldman N, & Yang Z (1994). A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular biology and evolution 11(5), 725-736. 10.1093/oxfordjournals.molbev.a040153
Description : M0 codon substitution model, also called as GY94, published by Goldman and Yang 1994
Find total 2 cited BEAST classes.
====== Package 17 : DENIM ======
Load classes from : ~/Library/Application Support/BEAST/2.5/DENIM/lib/denim.jar
denim.BirthDeathCollapseModel Jones GR, Aydin Z, and Oxelman B (2015). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics 31 (7) 991-998. DOI 10.1101/003178 http://bioinformatics.oxfordjournals.org/content/31/7/991.
Description : Birth-death-collapse distribution of prior for species tree or minimal clusters tree.
denim.CoalescenceMigrationDistribution Graham Jones (2017). Divergence estimation in the presence of ILS and migration. http://www.indriid.com
Description : Main DENIM class. Calculates coalescence-migration probability.
Find total 2 cited BEAST classes.
====== Package 18 : SA ======
Load classes from : ~/Library/Application Support/BEAST/2.5/SA/lib/SA.v2.0.0.jar
beast.evolution.speciation.ParameterizedSABirthDeathModel Gavryushkina A, Welch D, Stadler T, Drummond AJ (2014) Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol 10(12): e1003919. doi:10.1371/journal.pcbi.1003919
Description : Calculate tree density under Birth Death Sampling Through Time Model for Epidemics that is the BDM where an individual is sampled at a time with a constant rate psi and where an individual becomes noninfectious immediately after the samplingwith a constant probability r
beast.evolution.speciation.SABDSamplingThroughTimeModel Gavryushkina A, Welch D, Stadler T, Drummond AJ (2014) Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol 10(12): e1003919. doi:10.1371/journal.pcbi.1003919
Description : Calculate tree density under Birth Death Sampling Through Time Model for Epidemics that is the BDM where an individual is sampled at a time with a constant rate psi and where an individual becomes noninfectious immediately after the samplingwith a constant probability r
beast.evolution.speciation.SABirthDeathModel Gavryushkina A, Welch D, Stadler T, Drummond AJ (2014) Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS Comput Biol 10(12): e1003919. doi:10.1371/journal.pcbi.1003919
Description : Calculate tree density under Birth Death Sampling Through Time Model for Epidemics that is the BDM where an individual is sampled at a time with a constant rate psi and where an individual becomes noninfectious immediately after the samplingwith a constant probability r
Find total 3 cited BEAST classes.
====== Package 19 : EpiInf ======
Load classes from : ~/Library/Application Support/BEAST/2.5/EpiInf/lib/EpiInf.v7.0.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/EpiInf/lib/feast.v5.0.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/EpiInf/lib/xchart-3.0.0.jar
epiinf.distribs.LeapingSMCTreeDensity Gabriel Leventhal, Timothy Vaughan, David Welch, Alexei Drummond, Tanja Stadler, "Exact phylodynamic inference using particle filtering", in preparation.
Description : Use SMC to estimate density of tree conditional on model parameters. This variant leaps over tree events.
epiinf.distribs.SMCTreeDensity Timothy Vaughan, Gabriel Leventhal, David Welch, Alexei Drummond, Tanja Stadler, "Directly estimating epidemic curves from genomic data", preprint DOI:10.1101/142570
Description : Use SMC to estimate density of tree conditional on model parameters.
Find total 2 cited BEAST classes.
====== Package 20 : Mascot ======
Load classes from : ~/Library/Application Support/BEAST/2.5/Mascot/lib/guava-15.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/Mascot/lib/jblas-1.2.3.jar Load classes from : ~/Library/Application Support/BEAST/2.5/Mascot/lib/Mascot.v1.0.0.jar
beast.mascot.distribution.Mascot Nicola F. Müller, David A. Rasmussen, Tanja Stadler (2017) The Structured Coalescent and its Approximations. Mol Biol Evol 2017 msx186. doi: 10.1093/molbev/msx186
Description : Calculates the probability of a beast.tree using under the framework of Mueller (2017).
beast.mascot.distribution.MascotCollaps Nicola F. Müller, David A. Rasmussen, Tanja Stadler (2017) The Structured Coalescent and its Approximations. Mol Biol Evol 2017 msx186. doi: 10.1093/molbev/msx186
Description : Calculates the probability of a beast.tree using under the framework of Mueller (2017).
Find total 2 cited BEAST classes.
====== Package 21 : MASTER ======
Load classes from : ~/Library/Application Support/BEAST/2.5/MASTER/lib/guava-16.0.1.jar Load classes from : ~/Library/Application Support/BEAST/2.5/MASTER/lib/jackson-annotations-2.2.3.jar Load classes from : ~/Library/Application Support/BEAST/2.5/MASTER/lib/jackson-core-2.2.3.jar Load classes from : ~/Library/Application Support/BEAST/2.5/MASTER/lib/jackson-databind-2.2.3.jar Load classes from : ~/Library/Application Support/BEAST/2.5/MASTER/lib/MASTER.package.v6.0.0.jar
master.BeastTreeFromMaster Tim Vaughan and Alexei Drummond, 'A Stochastic Simulator of BirthâDeath Master Equations with Application to Phylodynamics'. Mol Biol Evol (2013) 30 (6): 1480-1493.
Description : Plugin which uses a MASTER simulation to construct a BEAST 2 tree. This only works when MASTER output is tree-like.
Find total 1 cited BEAST classes.
====== Package 22 : MGSM ======
Load classes from : ~/Library/Application Support/BEAST/2.5/MGSM/lib/MGSM.addon.jar
Find total 0 cited BEAST classes.
====== Package 23 : MM ======
Load classes from : ~/Library/Application Support/BEAST/2.5/MM/lib/MM.addon.jar
beast.evolution.substitutionmodel.LewisMK Lewis, Paul O. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic biology 50.6 (2001): 913-925.
Description : LewisMK subtitution model: equal rates, equal frequencies
Find total 1 cited BEAST classes.
====== Package 24 : MODEL_SELECTION ======
Load classes from : ~/Library/Application Support/BEAST/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar
beast.gss.GeneralisedSteppingStoneStep Xie, W., Lewis, P. O., Fan, Y., Kuo, L., & Chen, M. H. (2011). Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Systematic biology, 60(2), 150-160. 10.1093/sysbio/syq085
Description : Calculate marginal likelihood through generalised path sampling for a single step
beast.inference.PairedPathSamplingStep Lartillot, N., & Philippe, H. (2006). Computing Bayes factors using thermodynamic integration. Systematic biology, 55(2), 195-207. 10.1080/10635150500433722
Description : Calculate marginal likelihood through path sampling for a single step when comparing two models
beast.inference.PathSamplingStep Lartillot, N., & Philippe, H. (2006). Computing Bayes factors using thermodynamic integration. Systematic biology, 55(2), 195-207. 10.1080/10635150500433722
Description : Calculate marginal likelihood through path sampling for a single step
Find total 3 cited BEAST classes.
====== Package 25 : NS ======
Load classes from : /Users/dxie004/Library/Application Support/BEAST/2.5/NS/lib/NS.addon.jar
beast.gss.MultiThreadedNS Patricio Maturana, Brendon J. Brewer, Steffen Klaere, Remco Bouckaert. Model selection and parameter inference in phylogenetics using Nested Sampling. Systematic Biology, In Press 2018
Description : Multi threaded nested sampling
beast.gss.NS Patricio Maturana, Brendon J. Brewer, Steffen Klaere, Remco Bouckaert. Model selection and parameter inference in phylogenetics using Nested Sampling. Systematic Biology, In Press 2018
Description : Nested sampling for phylogenetics
beast.gss.NSThread Patricio Maturana, Brendon J. Brewer, Steffen Klaere, Remco Bouckaert. Model selection and parameter inference in phylogenetics using Nested Sampling. Systematic Biology, In Press 2018
Description : class for performing a one-threaded NS as part of MultiThreadedNS
Find total 3 cited BEAST classes.
====== Package 26 : PhyDyn ======
Load classes from : ~/Library/Application Support/BEAST/2.5/PhyDyn/lib/jblas-1.2.3.jar Load classes from : ~/Library/Application Support/BEAST/2.5/PhyDyn/lib/PhyDyn.v1.2.0.jar
phydyn.distribution.STreeLikelihood Erik M. Volz. 2012. Complex population dynamics and the coalescent under neutrality.Genetics. 2013 Nov;195(3):1199.
Description : Calculates the probability of a beast.tree under a structured population model using the framework of Volz (2012).
phydyn.distribution.STreeLikelihoodConstant Erik M. Volz. 2012. Complex population dynamics and the coalescent under neutrality.Genetics. 2013 Nov;195(3):1199.
Description : Not documented!!!
phydyn.distribution.STreeLikelihoodODE Erik M. Volz. 2012. Complex population dynamics and the coalescent under neutrality.Genetics. 2013 Nov;195(3):1199.
Description : Not documented!!!
Find total 3 cited BEAST classes.
====== Package 27 : phylodynamics ======
Load classes from : ~/Library/Application Support/BEAST/2.5/phylodynamics/lib/phylodynamics.addon.jar
beast.phylodynamics.BDSIR Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth–death SIR model. Denise Kuehnert, Tanja Stadler, Timothy Vaughan, and Alexei Drummond, J. R. Soc. Interface, 11:20131106 (2014).
Description : Phylodynamic tree prior that couples compartmental models (e.g. SIR, SIRS) with a piecewise constant birth-death-sampling process.
Find total 1 cited BEAST classes.
====== Package 28 : PoMo ======
Load classes from : ~/Library/Application Support/BEAST/2.5/PoMo/lib/PoMo.v1.0.1.jar
beast.evolution.substitutionmodel.PoMoGeneral De Maio, Schloetterer and Kosiol (2013). Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models. Molecular Biology and Evolution 30(10), 2249-2262.
De Maio, Schrempf and Kosiol (2015). PoMo: An Allele Frequency-Based Approach for Species Tree Estimation. Systematic Biology doi: 10.1093/sysbio/syv048.
Description : Specifies transition probability matrix for PoMo. Not in general reversible, unless fitnesses are equal and root frequencies are not estimated.
Find total 1 cited BEAST classes.
====== Package 29 : RBS ======
Load classes from : ~/Library/Application Support/BEAST/2.5/RBS/lib/RBS.addon.jar
beast.evolution.substitutionmodel.RB Bouckaert, Remco, Monica V. Alvarado-Mora, and J. R. Pinho. Evolutionary rates and HBV: issues of rate estimation with Bayesian molecular methods. Antiviral therapy 18.3 Pt B (2012): 497-503.
Description : Substitution model for nucleotides that changes where the count input determines the number of parameters used in a hierarchy of models
beast.evolution.substitutionmodel.VS Alexei J. Drummond and Remco R. Bouckaert. Bayesian evolutionary analysis with BEAST 2. CUP. 2014
Description : Substitution model for nucleotides that changes where the count input determines the number of parameters used in a hierarchy of models
Find total 2 cited BEAST classes.
====== Package 30 : SCOTTI ======
Load classes from : ~/Library/Application Support/BEAST/2.5/SCOTTI/lib/guava-15.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/SCOTTI/lib/jblas-1.2.3.jar Load classes from : ~/Library/Application Support/BEAST/2.5/SCOTTI/lib/SCOTTI.v2.0.0.jar
multitypetreeVolz.distributions.StructuredCoalescentTreeDensityNew Structured COalescent Transmission Tree Inference (SCOTTI). De Maio N., Wu C., Wilson D., PLOS Computational Biology 2016
Description : Likelihood of Coalescent tree (Volz-type) under the Volz approximation to the structured coalescent, fast version under the assumption that all demes have the same popsize and migration rates.
Find total 1 cited BEAST classes.
====== Package 31 : SNAPP ======
Load classes from : ~/Library/Application Support/BEAST/2.5/SNAPP/lib/snap.addon.jar
snap.MCMC Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : Allow sampling from the prior.
snap.ML Bouckaert RR, Heled J, Kuehnert D, Vaughan TG, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10(4): e1003537 10.1371/journal.pcbi.1003537
Description : Maximum likelihood search by hill climbing.
snap.likelihood.BetaApproximationLikelihood
Description : Implementation of Siren et al. Beta SNP approximation using Hiscott et al. integrator
snap.likelihood.SnAPTreeLikelihood David Bryant, Remco Bouckaert, Joseph Felsenstein, Noah Rosenberg, Arindam RoyChoudhury. Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis. Mol. Biol. Evol. 29(8):1917-1932, 2012 10.1016/j.ympev.2011.10.01
Description : Implements a tree Likelihood Function for Single Site Sorted-sequences on a tree.
snap.likelihood.ThresholdTreeLikelihood
Description : Implementation of Felsentstein's theshold model
Find total 5 cited BEAST classes.
====== Package 32 : SpeciesNetwork ======
Load classes from : ~/Library/Application Support/BEAST/2.5/SpeciesNetwork/lib/guava-21.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/SpeciesNetwork/lib/speciesnetwork.package.jar
speciesnetwork.Network Zhang C., Ogilvie H.A., Drummond A.J., Stadler T. (2018). Bayesian inference of species networks from multilocus sequence data. Molecular Biology and Evolution 35(2):504–517.
Description : Network representing reticulate evolution of species
speciesnetwork.NetworkParser Zhang C., Ogilvie H.A., Drummond A.J., Stadler T. (2018). Bayesian inference of species networks from multilocus sequence data. Molecular Biology and Evolution 35(2):504–517.
Description : Parse the network of extended Newick format.
Find total 2 cited BEAST classes.
====== Package 33 : SSM ======
Load classes from : ~/Library/Application Support/BEAST/2.5/SSM/lib/SSM.v1.1.0.jar
Find total 0 cited BEAST classes.
====== Package 34 : STACEY ======
Load classes from : ~/Library/Application Support/BEAST/2.5/STACEY/lib/stacey.jar
stacey.BirthDeathCollapseModel Jones GR, Aydin Z, and Oxelman B (2015). DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics 31 (7) 991-998. DOI 10.1101/003178 http://bioinformatics.oxfordjournals.org/content/31/7/991.
Description : Birth-death-collapse distribution of prior for species tree or minimal clusters tree.
stacey.PIOMSCoalescentDistribution Graham Jones (2016). Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology. DOI 10.1007/s00285-016-1034-0 http://link.springer.com/article/10.1007/s00285-016-1034-0
Description : The STACEY coalescent distribution. The central class in STACEY.
Find total 2 cited BEAST classes.
====== Package 35 : starbeast2 ======
Load classes from : ~/Library/Application Support/BEAST/2.5/starbeast2/lib/guava-23.0.jar Load classes from : ~/Library/Application Support/BEAST/2.5/starbeast2/lib/starbeast2.addon.jar
Find total 0 cited BEAST classes.
====== Package 36 : substBMA ======
Load classes from : ~/Library/Application Support/BEAST/2.5/substBMA/lib/colt.jar Load classes from : ~/Library/Application Support/BEAST/2.5/substBMA/lib/substBMA.v1.2.2.jar
beast.evolution.branchratemodel.SynchronizableUCRelaxedClock Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biol 4(5): e88 10.1371/journal.pbio.0040088
Description : Defines an uncorrelated relaxed molecular clock.
beast.evolution.likelihood.DummyTempWVTreeLikelihood Wu C-H, Suchard MA, Drummond AJ (2013) Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments. MBE 30(3):669-688.
Description : This class is well useful for testing purpose.
beast.evolution.likelihood.MultiAlignmentTempWVTreeLikelihood Wu C-H, Suchard MA, Drummond AJ (2013) Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments. MBE 30(3):669-688.
Description : Temporary likelihood calculation class that is able to take up multiple alignments.
beast.evolution.likelihood.NewWVTreeLikelihood Wu C-H, Suchard MA, Drummond AJ (2013) Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments. MBE 30(3):669-688.
Description : Tree likelihood supports alignment pattern weights to change during the MCMC.
beast.evolution.likelihood.SepTempWVTreeLikelihood Wu C-H, Suchard MA, Drummond AJ (2013) Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments. MBE 30(3):669-688.
Description : The tree likelihood used by the operators when using independent DPPs to the substitution model and rate partitioning. It allows pattern weights to be modified.
beast.evolution.likelihood.TempWVTreeLikelihood Wu C-H, Suchard MA, Drummond AJ (2013) Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments. MBE 30(3):669-688.
Description : Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. Pattern weights can be modified.
beast.evolution.tree.coalescent.ScaledBayesianSkyline Drummond, A. J., Rambaut, A., Shapiro, B. E. T. H., & Pybus, O. G. (2005). Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular biology and evolution, 22(5), 1185-1192. 10.1093/molbev/msi103
Description : Not documented!!!
Find total 7 cited BEAST classes.
====== Summary ======
Find 36 BEAST packages, processed 36. Find total 97 cited BEAST classes.
rbouckaert
There is already
@Citationannotation created forBEASTObject, to link the publication to the model and implementation.I created
PackageCitationsto pull out all citations from installed packages, which could be used to summarise the current package citations, or think about how to improve these citations.Another step of #770.