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@tgvaughan @rbouckaert @walterxie @bjoelle @igococha @MarnusStoltz @nicfel @zhangchicool @boskovav @jscire @4ment @genomescale
<!-- Package file for v2.6.X packages -->
<!-- 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='BEAST' version='2.6.2'
url="https://github.com/CompEvol/beast2/releases/download/v2.6.2/BEAST.package.v2.6.2.zip"
projectURL="http://beast2.org"
description="BEAST core"/>
<package name='BEAST' version='2.6.3'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEAST/BEAST.package.v2.6.3.zip"
projectURL="http://beast2.org"
description="BEAST package"/>
<package name='BEAST' version='2.6.4'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEAST/BEAST.package.v2.6.4.zip"
projectURL="http://beast2.org"
description="BEAST package"/>
<package name='BEAST' version='2.6.5'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEAST/BEAST.package.v2.6.5.zip"
projectURL="http://beast2.org"
description="BEAST package"/>
<package name='BEAST' version='2.6.6'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEAST/BEAST.package.v2.6.6.zip"
projectURL="http://beast2.org"
description="BEAST package"/>
<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='BEASTLabs' version='1.9.1'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.9.0/BEASTlabs.addon.v1.9.1.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='BEASTLabs' version='1.9.2'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.9.0/BEASTlabs.addon.v1.9.2.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='BEASTLabs' version='1.9.3'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.9.0/BEASTlabs.addon.v1.9.3.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='BEASTLabs' version='1.9.4'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.9.0/BEASTlabs.addon.v1.9.4.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='BEASTLabs' version='1.9.5'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEASTLabs/BEASTlabs.addon.v1.9.5.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='BEASTLabs' version='1.9.6'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEASTLabs/BEASTlabs.addon.v1.9.6.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='BEASTLabs' version='1.9.7'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEASTLabs/BEASTlabs.addon.v1.9.7.zip"
projectURL="https://github.com/BEAST2-Dev/BEASTLabs/"
description="BEAST utilities, such as Script, multi monophyletic constraints">
<depends on='beast2' atleast='2.6.6' atmost='2.6.9'/>
</package>
<package name='Beasy' version='0.0.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/Beasy/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='Babel' version='0.3.1'
url="https://raw.githubusercontent.com/CompEvol/packages/main/Babel/Babel.addon.v0.3.1.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name='Babel' version='0.3.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/Babel/Babel.addon.v0.3.2.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.6'/>
</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://raw.githubusercontent.com/CompEvol/packages/main/bModelTest/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='SNAPP' version='1.5.1'
url="https://raw.githubusercontent.com/CompEvol/packages/main/SNAPP/SNAPP.addon.v1.5.1.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='SNAPP' version='1.5.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/SNAPP/SNAPP.addon.v1.5.2.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='snapper' version='1.0.0'
url="https://raw.githubusercontent.com/CompEvol/packages/main/snapper/snapper.addon.v1.0.0.zip"
description="Diffusion based SNP and AFLP Phylogenies"
projectURL="https://github.com/rbouckaert/snapper">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='snapper' version='1.0.1'
url="https://github.com/rbouckaert/snapper/raw/master/dist/snapper.addon.v1.0.1.zip"
description="Diffusion based SNP and AFLP Phylogenies"
projectURL="https://github.com/rbouckaert/snapper">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='SNAPP' atleast='1.5.1'/>
</package>
<package name='snapper' version='1.0.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/snapper/snapper.addon.v1.0.2.zip"
description="Diffusion based SNP and AFLP Phylogenies"
projectURL="https://github.com/rbouckaert/snapper">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='SNAPP' atleast='1.5.1'/>
</package>
<package name='BEAST_CLASSIC' version='1.5.0'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BEAST_CLASSIC/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="MODEL_SELECTION" version="1.5.2"
url="https://github.com/BEAST2-Dev/model-selection/releases/download/v1.5.0/MODEL_SELECTION.addon.v1.5.2.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="1.5.3"
url="https://raw.githubusercontent.com/CompEvol/packages/main/MODEL_SELECTION/MODEL_SELECTION.addon.v1.5.3.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://raw.githubusercontent.com/CompEvol/packages/main/NS/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://raw.githubusercontent.com/CompEvol/packages/main/GEO_SPHERE/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='2.6.0' atmost='2.6.9'/>
</package>
<package name='SpeciesNetwork' version='0.13.0'
url="https://raw.githubusercontent.com/CompEvol/packages/main/SpeciesNetwork/SpeciesNetwork.zip"
description="Multispecies network coalescent (MSNC) inference of introgression and hybridization"
projectURL="https://github.com/zhangchicool/speciesnetwork">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='bacter' version='2.2.3'
url="https://raw.githubusercontent.com/CompEvol/packages/main/bacter/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='bacter' version='2.2.4'
url="https://raw.githubusercontent.com/CompEvol/packages/main/bacter/bacter.v2.2.4.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='bacter' version='2.2.5'
url="https://raw.githubusercontent.com/CompEvol/packages/main/bacter/bacter.v2.2.5.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='EpiInf' version='7.2.0'
url="https://github.com/tgvaughan/epiinf/releases/download/v7.2.0/EpiInf.v7.2.0.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='7.4.0'
url="https://github.com/tgvaughan/epiinf/releases/download/v7.4.0/EpiInf.v7.4.0.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='7.5.0'
url="https://github.com/tgvaughan/epiinf/releases/download/v7.5.0/EpiInf.v7.5.0.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='7.5.1'
url="https://github.com/tgvaughan/epiinf/releases/download/v7.5.1/EpiInf.v7.5.1.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='7.5.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/EpiInf/EpiInf.v7.5.2.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='MASTER' version='6.1.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/MASTER/MASTER.package.v6.1.2.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='MultiTypeTree' version='7.0.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/MultiTypeTree/MultiTypeTree.v7.0.2.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='bdmm' version='1.0'
url="https://raw.githubusercontent.com/CompEvol/packages/main/bdmm/BDMM.v1.0.zip"
description="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://raw.githubusercontent.com/CompEvol/packages/main/substBMA/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='BDSKY' version='1.4.6'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BDSKY/BDSKY.v1.4.6.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='BDSKY' version='1.4.7'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BDSKY/BDSKY.v1.4.7.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://raw.githubusercontent.com/CompEvol/packages/main/phylodynamics/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"
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<depends on='beast2' atleast='2.6.0' atmost="2.6.9"/>
<depends on='BEASTLabs' atleast='1.9.5'/>
<depends on='FastRelaxedClockLogNormal' atleast='1.1.0'/>
</package>
<package name='ORC' version='1.0.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/ORC/ORC.addon.v1.0.2.zip"
description="Optimised Relaxed Clock model"
projectURL="https://github.com/jordandouglas/ORC/">
<depends on='beast2' atleast='2.6.0' atmost="2.6.9"/>
<depends on='BEASTLabs' atleast='1.9.5'/>
<depends on='FastRelaxedClockLogNormal' atleast='1.1.1'/>
</package>
</packages>