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packages-extra.xml
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<packages>
<package name='Babel' version='0.1.1'
url="https://github.com/rbouckaert/Babel/releases/download/0.0.1/Babel.addon.v0.1.1.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.5.3'/>
</package>
<package name='Babel' version='0.1.3'
url="https://github.com/rbouckaert/Babel/releases/download/0.0.1/Babel.addon.v0.1.3.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
</package>
<package name='Babel' version='0.1.4'
url="https://github.com/rbouckaert/Babel/releases/download/0.0.1/Babel.addon.v0.1.4.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
</package>
<package name='Babel' version='0.1.5'
url="https://github.com/rbouckaert/Babel/releases/download/0.0.1/Babel.addon.v0.1.5.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
</package>
<package name='Babel' version='0.1.6'
url="https://github.com/rbouckaert/Babel/releases/download/0.0.1/Babel.addon.v0.1.6.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
</package>
<package name='Babel' version='0.1.7'
url="https://github.com/rbouckaert/Babel/releases/download/0.0.1/Babel.addon.v0.1.7.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
</package>
<package name='Babel' version='0.2.0'
url="https://github.com/rbouckaert/Babel/releases/download/v0.2.0/Babel.addon.v0.2.0.zip"
description="BABEL = BEAST analysis backing effective linguistics"
projectURL="https://github.com/rbouckaert/Babel">
<depends on='beast2' atleast='2.5.0'/>
<depends on='BEASTLabs' atleast='1.8.0'/>
</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'/>
<depends on='BEASTLabs' atleast='1.8.0'/>
</package>
<package name='LanguageSequenceGen' version='0.1.0'
url="https://github.com/lutrasdebtra/Beast-Borrowing-Plugin/releases/download/v0.1.0/LanguageSequenceGen.addon.v0.1.0.zip"
description="generates synthetic language data"
projectURL="https://github.com/lutrasdebtra/Beast-Borrowing-Plugin">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on="BEASTLabs" atleast="1.6.0"/>
</package>
<package name="correlatedcharacters" version="1.2.0"
url="https://github.com/Anaphory/correlatedcharacters/releases/download/v1.2.0/correlatedcharacters.v1.2.0.zip"
description="implementing elements of Pagel & Meade='s CorrelatedEvolution: A reversible substitution model for correlated morphological characters"
projectURL="https://github.com/Anaphory/correlatedcharacters">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
</package>
<package name="parameterclone" version="1.0.2"
url="https://github.com/Anaphory/parameterclone/releases/download/v1.0.2/parameterclone.v1.0.2.zip"
description="implementing Merge and Split operators for reversible-jump markov chains selecting models with various parameter size"
projectURL="https://github.com/Anaphory/parameterclone">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
</package>
<package name="TreeSetAnalyser" version="0.0.1"
url="https://github.com/rbouckaert/TreeSetAnalyser/releases/download/v0.0.1/TreeSetAnalyser.addon.v0.0.1.zip"
description="analyses with a fixed tree or set of trees"
projectURL="https://github.com/rbouckaert/TreeSetAnalyser">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on='BEAST_CLASSIC' atleast='1.4.0'/>
</package>
<package name="TreeSetAnalyser" version="0.0.2"
url="https://github.com/rbouckaert/TreeSetAnalyser/releases/download/v0.0.1/TreeSetAnalyser.addon.v0.0.2.zip"
description="analyses with a fixed tree or set of trees"
projectURL="https://github.com/rbouckaert/TreeSetAnalyser">
<depends on='beast2' atleast='2.5.0'/>
<depends on='BEASTLabs' atleast='1.7.0'/>
<depends on='BEAST_CLASSIC' atleast='1.3.0'/>
<depends on='NS' atleast='0.0.1'/>
<depends on='Babel' atleast='0.2.0'/>
</package>
<package name="TreeSetAnalyser" version="0.0.3"
url="https://github.com/rbouckaert/TreeSetAnalyser/releases/download/v0.0.1/TreeSetAnalyser.addon.v0.0.3.zip"
description="analyses with a fixed tree or set of trees"
projectURL="https://github.com/rbouckaert/TreeSetAnalyser">
<depends on='beast2' atleast='2.5.0'/>
<depends on='BEASTLabs' atleast='1.7.0'/>
<depends on='BEAST_CLASSIC' atleast='1.3.0'/>
<depends on='NS' atleast='0.0.1'/>
<depends on='Babel' atleast='0.2.0'/>
</package>
<package name="TreeSetAnalyser" version="0.0.4"
url="https://github.com/rbouckaert/TreeSetAnalyser/releases/download/v0.0.1/TreeSetAnalyser.addon.v0.0.4.zip"
description="analyses with a fixed tree or set of trees"
projectURL="https://github.com/rbouckaert/TreeSetAnalyser">
<depends on='beast2' atleast='2.6.3'/>
<depends on='BEASTLabs' atleast='1.9.4'/>
<depends on='BEAST_CLASSIC' atleast='1.5.0'/>
<depends on='NS' atleast='0.0.1'/>
<depends on='Babel' atleast='0.3.1'/>
</package>
<package name="EpochClockModel" version="0.0.1"
url="https://github.com/rbouckaert/EpochClockModel/releases/download/v0.0.1/EpochClockModel.v0.0.1.zip"
description="clock model that applies different relative rates accross different epochs"
projectURL="https://github.com/rbouckaert/EpochClockModel">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
</package>
<package name='OBAMA' version='0.0.1'
url="https://github.com/rbouckaert/obama/releases/download/v0.0.1/OBAMA.addon.v0.0.1.zip"
description="OBAMA Bayesian Amino-acid Model Averaging"
projectURL="https://github.com/rbouckaert/obama/">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
<depends on='bModelTest' atleast='1.0.3'/>
<depends on='BEASTLabs' atleast='1.5.3'/>
</package>
<package name='OBAMA' version='0.1.0'
url="https://github.com/rbouckaert/obama/releases/download/v0.1.0/OBAMA.addon.v0.1.0.zip"
description="OBAMA Bayesian Amino-acid Model Averaging"
projectURL="https://github.com/rbouckaert/obama/">
<depends on='beast2' atleast='2.5.0' atmost='2.5.9'/>
<depends on='bModelTest' atleast='1.1.0'/>
<depends on='BEASTLabs' atleast='1.8.0'/>
</package>
<package name="TreeStat2" version="0.0.1"
url="https://github.com/alexeid/TreeStat2/releases/download/v0.0.1/TreeStat2.v0.0.1.zip"
description="Utility for calculating tree statistics from tree log file"
projectURL="https://github.com/alexeid/TreeStat2/">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
</package>
<package name="TMA" version="0.0.1"
url="https://github.com/sebastianduchene/tree_model_adequacy/releases/download/v0.0.1/TMA.v0.0.1.zip"
description="Tree model adequacy: test whether the tree prior used is adequate for your data"
projectURL="https://github.com/sebastianduchene/tree_model_adequacy/">
<depends on='beast2' atleast='2.4.6' atmost='2.4.9'/>
<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="SMA" version="0.0.1"
url="https://github.com/rbouckaert/SMA/releases/download/v0.0.1/SMA.v0.0.1.zip"
description="Substitution model adequacy: test whether the substitution model used is adequate for your data"
projectURL="https://github.com/rbouckaert/SMA">
<depends on='beast2' atleast='2.4.6' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.7.1'/>
</package>
<package name="BREAK_AWAY" version="0.0.1"
url="https://github.com/rbouckaert/break-away/releases/download/v0.0.1/BREAK_AWAY.addon.v0.0.1.zip"
description="break-away model of phylogegraphy"
projectURL="https://github.com/rbouckaert/break-away">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
<depends on='GEO_SPHERE' atleast='1.1.1'/>
</package>
<package name="BADTRIP" version="0.1.0"
url="https://bitbucket.org/nicofmay/badtrip/raw/d30f5899fe17d2e69e0413a6323b654fda45ce29/dist/BADTRIP.v0.1.0.zip"
description="Infer transmission time for non-haplotype data and epi data"
projectURL="https://bitbucket.org/nicofmay/badtrip">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
</package>
<package name="BADTRIP" version="0.1.1"
url="https://bitbucket.org/nicofmay/badtrip/raw/14550c0e70a50374a1ac9a527f885283d727fdf7/dist/BADTRIP.v0.1.1.zip"
description="Infer transmission time for non-haplotype data and epi data"
projectURL="https://bitbucket.org/nicofmay/badtrip">
<depends on='beast2' atleast='2.4.3' atmost='2.4.9'/>
</package>
<package name="AlmostDistributions" version="0.0.1"
url="https://github.com/rbouckaert/AlmostDistributions/releases/download/v0.0.1/AlmostDistributions.v0.0.1.zip"
description="Almost-distributions"
projectURL="https://github.com/rbouckaert/AlmostDistributions">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
</package>
<package name="AlmostDistributions" version="0.0.2"
url="https://github.com/rbouckaert/AlmostDistributions/releases/download/v0.0.1/AlmostDistributions.v0.0.2.zip"
description="Almost-distributions"
projectURL="https://github.com/rbouckaert/AlmostDistributions">
<depends on='beast2' atleast='2.5.0' atmost='2.5.9'/>
</package>
<package name="AlmostDistributions" version="0.0.4"
url="https://github.com/rbouckaert/AlmostDistributions/releases/download/v0.0.1/AlmostDistributions.v0.0.4.zip"
description="Almost-distributions"
projectURL="https://github.com/rbouckaert/AlmostDistributions">
<depends on='beast2' atleast='2.5.0' atmost='2.5.9'/>
</package>
<package name="AlmostDistributions" version="0.0.5"
url="https://github.com/rbouckaert/AlmostDistributions/releases/download/v0.0.1/AlmostDistributions.v0.0.5.zip"
description="Almost-distributions"
projectURL="https://github.com/rbouckaert/AlmostDistributions">
<depends on='beast2' atleast='2.5.0' atmost='2.5.9'/>
</package>
<package name="AlmostDistributions" version="0.0.6"
url="https://github.com/rbouckaert/AlmostDistributions/releases/download/v0.0.1/AlmostDistributions.v0.0.6.zip"
description="Almost-distributions"
projectURL="https://github.com/rbouckaert/AlmostDistributions">
<depends on='beast2' atleast='2.5.0' atmost='2.5.9'/>
</package>
<package name="AlmostDistributions" version="0.1.0"
url="https://raw.githubusercontent.com/CompEvol/packages/main/AlmostDistributions/AlmostDistributions.addon.v0.1.0.zip"
description="Almost-distributions"
projectURL="https://github.com/rbouckaert/AlmostDistributions">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
<depends on='BEASTLabs' atleast='1.9.0'/>
</package>
<package name="NS" version="0.0.1"
url="https://github.com/BEAST2-Dev/nested-sampling/releases/download/v0.0.1/NS.addon.v0.0.1.zip"
description="Nested sampling for model selection and posterior inference"
projectURL="https://github.com/BEAST2-Dev/nested-sampling/wiki">
<depends on='beast2' atleast='2.4.0' atmost='2.4.9'/>
</package>
<package name="NS" version="0.1.0"
url="https://github.com/BEAST2-Dev/nested-sampling/releases/download/v0.1.0/NS.addon.v0.1.0.zip"
description="Nested sampling for model selection and posterior inference"
projectURL="https://github.com/BEAST2-Dev/nested-sampling/wiki">
<depends on='beast2' atleast='2.5.0' atmost='2.5.9'/>
</package>
<package name="Plasmid" version="0.1.1"
url="https://bitbucket.org/nicofmay/plasmidtree/raw/72a4d4f35b368cce2c7f8f9945257e5fc50a91e6/dist/plasmidTree.v0.1.1.zip"
description="plasmid trees are variants of the clonal frame through losses and recombinations/gains"
projectURL="https://bitbucket.org/nicofmay/plasmidtree">
<depends on='beast2' atleast='2.5.0' atmost='2.5.9'/>
</package>
<package name='PoMoCoV' version='0.1.0'
url="http://indriid.com/2020/PoMoCoV.addon.v0.1.0.zip"
description="Polymorphism-aware phylodynamic analysis for SARS-CoV-2"
projectURL="http://indriid.com/software.html">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='PoMoCoV' version='0.2.0'
url="http://indriid.com/2020/PoMoCoV.addon.v0.2.0.zip"
description="Polymorphism-aware phylodynamic analysis for SARS-CoV-2"
projectURL="http://indriid.com/software.html">
<depends on='beast2' atleast='2.6.0' atmost='2.6.9'/>
</package>
<package name='FixedTreeAnalysis' version='0.0.1'
url="https://github.com/rbouckaert/FixedTreeAnalysis/releases/download/v0.0.1/FixedTreeAnalysis.addon.v0.0.1.zip"
description="Fixed tree and posterior tree set analysis"
projectURL="https://github.com/rbouckaert/FixedTreeAnalysis">
<depends on='beast2' atleast='2.6.3' atmost="2.6.9"/>
</package>
<package name='starbeast3' version='0.0.1'
url="https://github.com/CompEvol/packages/blob/main/StarBeast3/starbeast3.addon.v0.0.1.zip?raw=true"
description="StarBeast3 multi species coalescent using smart MCMC operators"
projectURL="https://github.com/rbouckaert/starbeast3">
<depends on='beast2' atleast='2.6.0' atmost="2.6.9"/>
<depends on='BEASTLabs' atleast='1.9.4'/>
<depends on='FastRelaxedClockLogNormal' atleast='1.0.0'/>
</package>
<package name='starbeast3' version='0.1.0'
url="https://raw.githubusercontent.com/CompEvol/packages/main/StarBeast3/starbeast3.addon.v0.1.0.zip"
description="StarBeast3 multi species coalescent using smart MCMC operators"
projectURL="https://github.com/rbouckaert/starbeast3">
<depends on='beast2' atleast='2.6.0' atmost="2.6.9"/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='FastRelaxedClockLogNormal' atleast='1.1.1'/>
<depends on='ORC' atleast='1.0.3'/>
</package>
<package name='speedemon' version='0.1.0'
url="https://raw.githubusercontent.com/CompEvol/packages/main/speedemon/speedemon.addon.v0.1.0.zip"
description="Fast species delimitation under the multispecies coalescent"
projectURL="https://github.com/rbouckaert/speedemon">
<depends on='beast2' atleast='2.6.6'/>
<depends on='snapper' atleast='1.0.2'/>
<depends on='BEASTLabs' atleast='1.9.7'/>
<depends on='ORC' atleast='1.0.3'/>
<depends on='BICEPS' atleast='0.0.2'/>
</package>
<package name='ORC' version='1.0.0'
url="https://github.com/jordandouglas/ORC/releases/download/v1.0.0/ORC.addon.v1.0.0.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='1.1.0'/>
</package>
<package name='BICEPS' version='0.0.1'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BICEPS/BICEPS.addon.v0.0.1.zip"
description="Bayesian Integrated Coalescent Epoch PlotS + Yule Skyline"
projectURL="https://github.com/rbouckaert/biceps/">
<depends on='beast2' atleast='2.6.4' atmost="2.6.9"/>
<depends on='BEASTLabs' atleast='1.9.5'/>
</package>
<package name='BICEPS' version='0.0.2'
url="https://raw.githubusercontent.com/CompEvol/packages/main/BICEPS/BICEPS.addon.v0.0.2.zip"
description="Bayesian Integrated Coalescent Epoch PlotS + Yule Skyline"
projectURL="https://github.com/rbouckaert/biceps/">
<depends on='beast2' atleast='2.6.4' atmost="2.6.9"/>
<depends on='BEASTLabs' atleast='1.9.5'/>
</package>
<package name="outercore" version="0.0.9"
url="https://raw.githubusercontent.com/LinguaPhylo/beast-outercore/master/releases/outercore.v0.0.9.zip"
projectURL="https://github.com/LinguaPhylo/beast-outercore"
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