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<!-- Package file for v2.6.X packages -->
<!-- NOTE: this is currently for testing the 2.6.0 prerelease only -->
<!-- NOTE: if you edit this file, DO NOT DELETE any entries. Older package versions -->
<!-- will be available for running BEAST files so that analyses can be replicated -->
<!-- with the package versions used in the original analysis. -->
<packages>
<package name='BEAST' version='2.6.0'
url="https://github.com/CompEvol/beast2/releases/download/v2.6.0/BEAST.v2.6.0.package.zip"
projectURL="http://beast2.org"
description="BEAST core"/>
<package name='BEAST' version='2.6.1'
url="https://github.com/CompEvol/beast2/releases/download/v2.6.1/BEAST.package.v2.6.1.zip"
projectURL="http://beast2.org"
description="BEAST core"/>
<package name='BEASTLabs' version='1.9.0'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.9.0/BEASTlabs.addon.v1.9.0.zip"
projectURL="https://github.com/BEAST2-Dev/BEASTLabs/"
description="BEAST utilities, such as Script, multi monophyletic constraints">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='Beasy' version='0.0.2'
url="https://github.com/rbouckaert/beasy/releases/download/v0.0.1/Beasy.v0.0.2.zip"
projectURL="https://github.com/rbouckaert/beasy"
description="Makes it easier to construct models: Automatic methods text generator, Beasy XML generator, and more">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name='Babel' version='0.2.1'
url="https://github.com/rbouckaert/Babel/releases/download/v0.2.0/Babel.addon.v0.2.1.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.8.0'/>
</package>
<package name='bModelTest' version='1.2.0'
url="https://github.com/BEAST2-Dev/bModelTest/releases/download/v1.2.0/bModelTest.addon.v1.2.0.zip"
description="Bayesian model test for nucleotide subst models, gamma rate heterogeneity and invariant sites"
projectURL="https://github.com/BEAST2-Dev/bModelTest/wiki">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name='bModelTest' version='1.2.1'
url="https://github.com/BEAST2-Dev/bModelTest/releases/download/v1.2.0/bModelTest.addon.v1.2.1.zip"
description="Bayesian model test for nucleotide subst models, gamma rate heterogeneity and invariant sites"
projectURL="https://github.com/BEAST2-Dev/bModelTest/wiki">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name='SNAPP' version='1.5.0'
url="https://github.com/BEAST2-Dev/SNAPP/releases/download/v1.5.0/SNAPP.addon.v1.5.0.zip"
description="SNP and AFLP Phylogenies"
projectURL="http://beast2.org/snapp/">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='BEAST_CLASSIC' version='1.5.0'
url="https://github.com/BEAST2-Dev/beast-classic/releases/download/v1.5.0/BEAST_CLASSIC.addon.v1.5.0.zip"
projectURL="https://github.com/BEAST2-Dev/beast-classic/"
description="BEAST classes ported from BEAST 1 in wrappers" >
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name="MODEL_SELECTION" version="1.5.0"
url="https://github.com/BEAST2-Dev/model-selection/releases/download/v1.5.0/MODEL_SELECTION.addon.v1.5.0.zip"
description="Select models through path sampling/stepping stone analysis"
projectURL="https://github.com/BEAST2-Dev/model-selection">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name="MODEL_SELECTION" version="1.5.1"
url="https://github.com/BEAST2-Dev/model-selection/releases/download/v1.5.0/MODEL_SELECTION.addon.v1.5.1.zip"
description="Select models through path sampling/stepping stone analysis"
projectURL="https://github.com/BEAST2-Dev/model-selection">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name="NS" version="1.1.0"
url="https://github.com/BEAST2-Dev/nested-sampling/releases/download/v1.1.0/NS.addon.v1.1.0.zip"
description="Nested sampling for model selection and posterior inference"
projectURL="https://github.com/BEAST2-Dev/nested-sampling/wiki">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
<depends on='MODEL_SELECTION' atleast='1.5.0'/>
</package>
<package name='GEO_SPHERE' version='1.3.0'
url="https://github.com/BEAST2-Dev/beast-geo/releases/download/v1.3.0/GEO_SPHERE.addon.v1.3.0.zip"
description="Whole world phylogeography"
projectURL="https://github.com/BEAST2-Dev/beast-geo">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name='SpeciesNetwork' version='0.12.2'
url="https://github.com/zhangchicool/speciesnetwork/releases/download/v0.12.2/SpeciesNetwork.zip"
description="Multispecies network coalescent (MSNC) inference of introgression and hybridization"
projectURL="https://github.com/zhangchicool/speciesnetwork">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='bacter' version='2.2.3'
url="https://github.com/tgvaughan/bacter/releases/download/v2.2.3/bacter.v2.2.3.zip"
description="Bacterial ARG inference."
projectURL="http://tgvaughan.github.io/bacter" >
<depends on='BEAST' atleast='2.6.0' atmost="2.6.9"/>
</package>
<package name='EpiInf' version='7.1.4'
url="https://github.com/tgvaughan/epiinf/releases/download/v7.1.4/EpiInf.v7.1.4.zip"
description="BD/SIR/SIS epidemic trajectory inference."
projectURL="http://tgvaughan.github.io/EpiInf" >
<depends on='BEAST' atleast='2.5.0' atmost="2.6.9"/>
<depends on='SA' atleast='2.0.0'/>
</package>
<package name='EpiInf' version='7.1.5'
url="https://github.com/tgvaughan/epiinf/releases/download/v7.1.5/EpiInf.v7.1.5.zip"
description="BD/SIR/SIS epidemic trajectory inference."
projectURL="http://tgvaughan.github.io/EpiInf" >
<depends on='BEAST' atleast='2.5.0' atmost="2.6.9"/>
<depends on='SA' atleast='2.0.0'/>
</package>
<package name='MASTER' version='6.1.1'
url="https://github.com/tgvaughan/MASTER/releases/download/v6.1.1/MASTER.package.v6.1.1.zip"
description="Stochastic population dynamics simulation"
projectURL="http://tgvaughan.github.io/MASTER" >
<depends on='beast2' atleast='2.6.0' atmost="2.6.9"/>
</package>
<package name='MultiTypeTree' version='7.0.1'
url="https://github.com/tgvaughan/MultiTypeTree/releases/download/v7.0.1/MultiTypeTree.v7.0.1.zip"
description="Structured coalescent inference"
projectURL="http://tgvaughan.github.io/MultiTypeTree" >
<depends on='BEAST' atleast='2.6.0' atmost="2.6.9"/>
</package>
<package name='bdmm' version='0.3.5'
url="https://github.com/denisekuehnert/bdmm/releases/download/0.3.5/BDMM.v0.3.5.zip"
description="pre-release of multitype birth-death model (aka birth-death-migration model)"
projectURL="https://github.com/denisekuehnert/bdmm" >
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='MASTER' atleast='6.0.1'/>
<depends on='MultiTypeTree' atleast='7.0.1'/>
</package>
<package name="substBMA" version="1.2.3"
url="https://github.com/jessiewu/substBMA/releases/download/v1.2.3/substBMA.v1.2.3.zip"
projectURL="https://github.com/jessiewu/substBMA"
description="Substitution Bayesian Model Averaging">
<depends on='beast2' atleast='2.5.0' atmost="2.6.9"/>
</package>
<package name='BDSKY' version='1.4.5'
url="https://github.com/BEAST2-Dev/bdsky/releases/download/1.4.5/BDSKY.addon.v1.4.5.zip"
projectURL="https://github.com/BEAST2-Dev/bdsky/"
description="birth death skyline - handles serially sampled tips, piecewise constant rate changes through time and sampled ancestors">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='phylodynamics' version='1.3.0'
url="https://github.com/BEAST2-Dev/phylodynamics/releases/download/1.3.0/phylodynamics.addon.1.3.0.zip"
projectURL="https://github.com/BEAST2-Dev/phylodynamics"
description="BDSIR and Stochastic Coalescent" >
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
<depends on='BDSKY' atleast='1.4.0' atmost='1.4.9'/>
</package>
<package name='STACEY' version='1.2.5'
url="http://indriid.com/2019/STACEY.addon.v1.2.5.zip"
description="Species delimitation and species tree estimation"
projectURL="http://indriid.com/software.html">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='DENIM' version='1.0.0'
url="http://indriid.com/2019/DENIM.addon.v1.0.0.zip"
description="Divergence Estimation Notwithstanding ILS and Migration"
projectURL="http://indriid.com/software.html">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name="BREAK_AWAY" version="1.0.0"
url="https://github.com/rbouckaert/break-away/releases/download/v1.0.0/BREAK_AWAY.addon.v1.0.0.zip"
description="break-away model of phylogegraphy"
projectURL="https://github.com/rbouckaert/break-away">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
<depends on='GEO_SPHERE' atleast='1.3.0'/>
</package>
<package name='BEASTvntr' version='0.1.3'
url="https://github.com/arjun-1/BEASTvntr/releases/download/v0.1.3/BEASTvntr.addon.v0.1.3.zip"
description="Variable Number of Tandem Repeat data, such as microsattelites"
projectURL="https://github.com/arjun-1/BEASTvntr">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='MGSM' version='0.3.0'
url="https://github.com/BEAST2-Dev/MGSM/releases/download/v0.3.0/MGSM.addon.v0.3.0.zip"
description="Multi-gamma and relaxed gamma site models"
projectURL="https://github.com/BEAST2-Dev/MGSM/wiki">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name="PhyDyn" version="1.3.4"
url="https://github.com/mrc-ide/PhyDyn/releases/download/v1.3.4/PhyDyn.v1.3.4.zip"
description="PhyDyn: Epidemiological modelling with BEAST"
projectURL="https://github.com/mrc-ide/PhyDyn">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='SSM' version='1.1.0'
url="https://github.com/BEAST2-Dev/substmodels/releases/download/v1.1.0/SSM.v1.1.0.zip"
description="Standard Nucleotide Substitution Models"
projectURL="https://github.com/BEAST2-Dev/substmodels/">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='CodonSubstModels' version='1.1.3'
url="https://github.com/BEAST2-Dev/codonsubstmodels/releases/download/v1.1.3/CodonSubstModels.v1.1.3.zip"
description="Codon substitution models"
projectURL="https://github.com/BEAST2-Dev/codonsubstmodels/">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='FLC' version='1.1.0'
url="https://github.com/4ment/flc/releases/download/v1.1.0/flc.v1.1.0.zip"
description="Flexible local clock model"
projectURL="https://github.com/4ment/flc">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='SA' version='2.0.2'
url="https://github.com/CompEvol/sampled-ancestors/releases/download/v2.0.2/SA.v2.0.2.zip"
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees" >
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.8.0'/>
</package>
<package name="Mascot" version="1.2.2"
url="https://github.com/nicfel/Mascot/releases/download/v1.2.2/Mascot.v1.2.2.zip"
description="Marginal approximation of the structured coalescent"
projectURL="https://taming-the-beast.org/tutorials/Mascot-Tutorial/">
<depends on="beast2" atleast="2.5.0" atmost='2.6.9'/>
</package>
<package name="CoupledMCMC" version="0.1.7"
url="https://github.com/nicfel/CoupledMCMC/releases/download/v0.1.7/CoupledMCMC.v0.1.7.zip"
description="Coupled MCMC (parallel Tempering or MC3)"
projectURL="https://github.com/nicfel/CoupledMCMC/">
<depends on="beast2" atleast="2.5.2" atmost='2.6.9'/>
<depends on="BEASTLabs" atleast="1.8.2"/>
</package>
<package name='MM' version='1.1.1'
url="https://github.com/CompEvol/morph-models/releases/download/untagged-74152ea8507b4e08d3ad/MM.addon.v1.1.1.zip"
projectURL="https://github.com/CompEvol/morph-models"
description="Enables models of morphological chatacter evolution">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='StarBEAST2' version='0.15.5'
url="https://github.com/genomescale/starbeast2/releases/download/v0.15.5/StarBEAST2.zip"
projectURL="https://github.com/genomescale/starbeast2"
description="Multispecies coalescent inference using multi-locus and fossil data">
<depends on="beast2" atleast="2.5.0" atmost="2.6.9"/>
<depends on="SA" atleast="2.0.0"/>
<depends on="MM" atleast="1.1.0"/>
</package>
<package name='BASTA' version='3.0.1'
url="https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/raw/dc8bee43b5a792a860d6fbc4d10ba39503e17c54/dist/BASTA.v3.0.1.zip"
description="Bayesian structured coalescent approximation"
projectURL="https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='SCOTTI' version='2.0.1'
url="https://bitbucket.org/nicofmay/scotti/raw/3db8fa07d32287922240324064dd8e6ab030a4cd/SCOTTI/dist/SCOTTI.v2.0.1.zip"
description="Structured COalescent Transmission Tree Inference"
projectURL="https://bitbucket.org/nicofmay/scotti">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name="BADTRIP" version="1.0.0"
url="https://bitbucket.org/nicofmay/badtrip/raw/4a69ce6b2ee092e451c72a291a54ae450ac90fc6/dist/BADTRIP.v1.0.0.zip"
description="Infer transmission time for non-haplotype data and epi data"
projectURL="https://bitbucket.org/nicofmay/badtrip">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='PoMo' version='1.0.1'
url="https://bitbucket.org/nicofmay/pomo-beast/raw/8eaa20892c8f3b3ce7f428a8a144b8d817838ad8/dist/PoMo.v1.0.1.zip"
description="PoMo, a substitution model that separates mutation and drift processes"
projectURL="https://bitbucket.org/nicofmay/pomo-beast">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='CA' version='2.0.0'
url="https://github.com/BEAST2-Dev/cladeage/releases/download/v.2.0.0/CA.addon.v2.0.0.zip"
description="Bayesian estimation of clade ages based on probabilities of fossil sampling"
projectURL="https://github.com/BEAST2-Dev/cladeage">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='MSBD' version='1.1.0'
url="https://bitbucket.org/bjoelle/msbd/raw/a20abf3c5dfd9f30041d4c9f2b57dcaf2e430189/dist/MSBD.v1.1.0.zip"
description="Multi-state birth-death prior with state-specific birth and death rates"
projectURL="https://bitbucket.org/bjoelle/msbd">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name="TreeStat2" version="0.0.2"
url="https://github.com/alexeid/TreeStat2/releases/download/v0.0.1/TreeStat2.v0.0.2.zip"
description="Utility for calculating tree statistics from tree log file"
projectURL="https://github.com/alexeid/TreeStat2/">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
<package name='TMA' version='1.0.0'
url="https://github.com/sebastianduchene/tree_model_adequacy/releases/download/v1.0.0/TMA.v1.0.0.zip"
projectURL="https://github.com/sebastianduchene/tree_model_adequacy"
description="Tree model adequacy: test whether the tree prior used is adequate for your data">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='MASTER' atleast='5.1.1'/>
<depends on='BEASTLabs' atleast='1.7.1'/>
<depends on='phylodynamics' atleast='1.2.1'/>
<depends on='BDSKY' atleast='1.3.3'/>
<depends on='TreeStat2' atleast='0.0.1'/>
</package>
<package name='CoalRe' version='0.0.4'
url="https://github.com/nicfel/CoalRe/releases/download/v0.0.4/CoalRe.v0.0.4.zip"
description="Infer viral reassortment networks"
projectURL="https://taming-the-beast.org/tutorials/Reassortment-Tutorial/">
<depends on='beast2' atleast='2.5.0' atmost='2.6.9'/>
</package>
</packages>
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