CBAN XML : (latest version all) packages
Extract 64 unique packages from packages2.7.xml
| Package | Version | Description | Dependency |
|---|---|---|---|
| Babel | 0.4.2 | BABEL = BEAST analysis backing effective linguistics | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), BEASTLabs (2.0.0-?) |
| bacter | 3.0.1 | Bacterial ARG inference. | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?), feast (9.0.0-?) |
| BADTRIP | 2.0.0 | Infer transmission time for non-haplotype data and epi data | BEAST.base (2.7.2-?) |
| BASTA | 4.0.0 | Bayesian structured coalescent approximation | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| bdmm | 2.0.0 | Multitype birth-death model (aka birth-death-migration model) | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?), MultiTypeTree (8.0.0-?), MASTER (7.0.0-?) |
| BDSKY | 1.5.1 | birth death skyline - handles serially sampled tips, piecewise constant rate changes through time and sampled ancestors | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| bdtree | 0.0.1 | Birth-death sequential sampling | BEAST.base (2.7.3-?), BEAST.app (2.7.3-?) |
| BEAST.app | 2.7.7 | BEAST base applications | BEAST.base (2.7.7-2.7.9) |
| BEAST.base | 2.7.7 | BEAST base | |
| BEAST_CLASSIC | 1.6.3 | BEAST classes ported from BEAST 1 in wrappers | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| BEASTLabs | 2.0.2 | BEAST utilities, such as Script, multi monophyletic constraints | BEAST.base (2.7.0-2.7.9), BEAST.app (2.7.0-?) |
| BEASTvntr | 0.2.0 | Variable Number of Tandem Repeat data, such as microsattelites | BEAST.base (2.7.1-?), BEAST.app (2.7.1-?) |
| BICEPS | 1.1.2 | Bayesian Integrated Coalescent Epoch PlotS + Yule Skyline | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| bModelTest | 1.3.3 | Bayesian model test for nucleotide subst models, gamma rate heterogeneity and invariant sites | BEAST.base (2.7.0-2.7.9), BEAST.app (2.7.0-?) |
| BREAK_AWAY | 1.2.0 | break-away model of phylogegraphy | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), BEASTLabs (2.0.0-?), GEO_SPHERE (1.4.0-?) |
| CA | 2.1.0 | Bayesian estimation of clade ages based on probabilities of fossil sampling | BEAST.base (2.7.3-?), BEAST.app (2.7.3-?) |
| CCD | 1.0.3 | Better tree distribution and point estimates, computation of entropy, rogues and more. | BEAST.base (2.7.7-?), BEAST.app (2.7.7-?) |
| ClaDS | 2.1.2 | Implementation of the ClaDS birth-death tree prior with sampled ancestors | BEAST.base (2.7.5-2.7.9), BEAST.app (2.7.5-2.7.9) |
| CoalRe | 1.0.4 | Inference of Recombination networks | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| CodonSubstModels | 2.0.0 | Codon substitution models for DNA | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| contacTrees | 1.2.0 | Phylogenetic model with horizontal transfer for linguistics | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), feast (9.0.0-?), BEASTLabs (2.0.0-?), BICEPS (1.1.0-?) |
| contraband | 1.0.1 | Scalable brownian models for continuous trait evolution | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| CoupledMCMC | 1.2.2 | Adaptive coupled MCMC (adaptive parallel tempering or MC3) | BEAST.base (2.7.5-?), BEAST.app (2.7.5-?) |
| CubeVB | 1.0.2 | Variational Bayes on a cube | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), BEASTLabs (2.0.0-?) |
| DENIM | 1.1.1 | Divergence Estimation Notwithstanding ILS and Migration | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| EpiInf | 8.0.0 | BD/SIR/SIS epidemic trajectory inference. | BEAST.base (2.7.1-2.7.9), BEAST.app (2.7.1-?), SA (2.1.0-?), feast (9.0.0-?) |
| FastRelaxedClockLogNormal | 1.2.0 | Relaxed clock that works well with large data | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| feast | 9.8.5 | Expands the flexibility of BEAST 2 XML. | BEAST.base (2.7.0-2.7.9), BEAST.app (2.7.0-2.7.9) |
| FixedTreeAnalysis | 0.0.2 | Analysis for a fixed tree or fixed tree set | BEAST.base (2.7.4-?), BEAST.app (2.7.4-?) |
| FLC | 1.2.0 | Flexible local clock model | BEAST.base (2.7.4-?), BEAST.app (2.7.4-?) |
| gammaspike | 1.0.0 | A clock model that captures and tests for punctuated evolution | BEAST.base (2.7.7-?), BEAST.app (2.7.7-?), SA (2.1.1-?) |
| GEO_SPHERE | 1.4.1 | Whole world phylogeography | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), BEASTLabs (2.0.0-?) |
| lphybeast | 1.2.1 | A command-line program that takes an LPhy model specification including a data block, and produces a BEAST 2 XML input file. | BEAST.base (2.7.7-?), BEAST.app (2.7.7-?), BEASTLabs (2.0.2-?), BEAST_CLASSIC (1.6.3-?), feast (9.8.5-?), SSM (1.2.0-?), ORC (1.2.0-?), bdtree (0.0.1-?) |
| LPhyBeastExt | 1.0.0 | An extension of LPhyBEAST. | lphybeast (1.2.0-?), Mascot (3.0.0-?), MM (1.2.1-?), SA (2.1.0-?) |
| Mascot | 3.0.7 | Marginal approximation of the structured coalescent | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| MASTER | 7.0.0 | Stochastic population dynamics simulation | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| MGSM | 0.4.0 | Multi-gamma and relaxed gamma site models | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| MM | 1.2.1 | Enables models of morphological chatacter evolution | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| MODEL_SELECTION | 1.6.2 | Select models through path sampling/stepping stone analysis | BEAST.base (2.7.5-?), BEAST.app (2.7.5-?) |
| MSBD | 2.0.4 | MSBD multi-type birth-death tree prior with sampled ancestors | BEAST.base (2.7.2-2.7.9), BEAST.app (2.7.2-2.7.9), MM (1.2.0-?) |
| MultiTypeTree | 8.2.0 | Structured coalescent inference. | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| NS | 1.2.2 | Nested sampling for model selection and posterior inference | BEAST.base (2.7.5-?), BEAST.app (2.7.5-?), MODEL_SELECTION (1.6.0-?) |
| OBAMA | 1.1.1 | OBAMA for Bayesian Amino-acid Model Averaging | BEAST.base (2.7.0-2.7.9), BEAST.app (2.7.0-?), bModelTest (1.3.0-?) |
| ORC | 1.2.0 | Optimised Relaxed Clock model | BEAST.base (2.7.5-?), BEAST.app (2.7.5-?), BEASTLabs (2.0.0-?) |
| PhyDyn | 1.4.0 | PhyDyn: Epidemiological modelling with BEAST | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| phylodynamics | 1.4.0 | BDSIR and Stochastic Coalescent | BEAST.base (2.7.0-?), BDSKY (1.5.0-?) |
| phylonco | 1.2.0 | A package for single cell cancer evolution. | BEAST.base (2.7.6-?), BEAST.app (2.7.6-?), BEASTLabs (2.0.2-?) |
| phylonco.lphybeast | 1.2.1 | A LPhyBEAST extension for phylonco (requires: LPhy and phylonco-lphy). | phylonco (1.2.0-?), lphybeast (1.2.1-?) |
| PIQMEE | 1.0.0 | Birth-death skyline-based method efficiently dealing with duplicate sequences | BEAST.base (2.7.1-?), BEAST.app (2.7.1-?), BDSKY (1.5.0-?) |
| PoMo | 1.1.1 | PoMo, a substitution model that separates mutation and drift processes | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| Recombination | 1.0.1 | Inference of Recombination networks | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| ReMASTER | 2.7.2 | Phylodynamic simulation system | BEAST.base (2.7.0-2.7.9), BEAST.app (2.7.0-2.7.9) |
| SA | 2.1.1 | Sampled ancestor trees | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), BEASTLabs (2.0.0-?) |
| SCOTTI | 3.0.0 | Structured COalescent Transmission Tree Inference | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| SNAPP | 1.6.1 | SNP and AFLP Phylogenies | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), BEASTLabs (2.0.0-?) |
| snapper | 1.1.5 | Diffusion based SNP and AFLP Phylogenies | BEAST.base (2.7.5-?), BEAST.app (2.7.5-?), SNAPP (1.6.0-?) |
| SpeciesNetwork | 1.0.0 | Multispecies network coalescent (MSNC) inference of introgression and hybridization | BEAST.base (2.7.3-?), BEAST.app (2.7.3-?) |
| speedemon | 1.1.0 | Fast species delimitation under the multispecies coalescent | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?), BEASTLabs (2.0.0-?), ORC (1.1.0-?), BICEPS (1.1.0-?) |
| SSM | 1.2.0 | Standard Nucleotide Substitution Models | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| STACEY | 1.3.1 | Species delimitation and species tree estimation | BEAST.base (2.7.0-?), BEAST.app (2.7.0-?) |
| StarBEAST2 | 1.0.0 | Multispecies coalescent inference using multi-locus and fossil data | BEAST.base (2.7.3-?), BEAST.app (2.7.3-?), SA (2.1.0-?), MM (1.2.1-?) |
| starbeast3 | 1.1.9 | StarBeast3 multispecies coalescent using advanced MCMC operators | BEAST.base (2.7.3-?), BEAST.app (2.7.3-?), BEASTLabs (2.0.0-?), SA (2.1.0-?), ORC (1.2.0-?) |
| timtam | 0.4.0 | Distribution for birth-death models with occurrence data and population size estimation. | BEAST.base (2.7.2-?), BEAST.app (2.7.2-?) |
| TreeStat2 | 0.2.0 | Utility for calculating tree statistics from tree log file | BEAST.base (2.7.7-?), BEAST.app (2.7.7-?), CCD (1.0.1-?) |
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