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packages.xml
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<!-- NOTE: if you edit this file, DO NOT DELETE any entries. From BEAST v2.4.5 onwards, 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='2.4.8'
url="https://github.com/CompEvol/beast2/releases/download/v2.4.8/BEAST.v2.4.8.addon.zip"
projectURL="http://beast2.org"
description="BEAST core"/>
<package name='BDSKY' version='1.3.2'
url="https://github.com/BEAST2-Dev/bdsky/releases/download/1.3.2/BDSKY.addon.1.3.2.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='2.4.0'/>
</package>
<package name='BDSKY' version='1.3.3'
url="https://github.com/BEAST2-Dev/bdsky/releases/download/1.3.3/BDSKY.addon.1.3.3.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='2.4.0'/>
</package>
<package name='BEASTLabs' version='1.5.3'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.5.0/BEASTlabs.addon.v1.5.3.zip"
projectURL="https://github.com/BEAST2-Dev/BEASTLabs/"
description="BEAST utilities, such as Script, multi monophyletic constraints">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='BEASTLabs' version='1.7.0'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.7.0/BEASTlabs.addon.v1.7.0.zip"
projectURL="https://github.com/BEAST2-Dev/BEASTLabs/"
description="BEAST utilities, such as Script, multi monophyletic constraints">
<depends on='beast2' atleast='2.4.3'/>
</package>
<package name='BEASTLabs' version='1.7.1'
url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v1.7.0/BEASTlabs.addon.v1.7.1.zip"
projectURL="https://github.com/BEAST2-Dev/BEASTLabs/"
description="BEAST utilities, such as Script, multi monophyletic constraints">
<depends on='beast2' atleast='2.4.3'/>
</package>
<package name='BEAST_CLASSIC' version='1.3.0'
url="https://github.com/BEAST2-Dev/beast-classic/releases/download/v1.3.0/BEAST_CLASSIC.addon.v1.3.0.zip"
projectURL="https://github.com/BEAST2-Dev/beast-classic/"
description="BEAST classes ported from BEAST 1 in wrappers" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.4.0'/>
</package>
<package name='BEAST_CLASSIC' version='1.3.1'
url="https://github.com/BEAST2-Dev/beast-classic/releases/download/v1.3.0/BEAST_CLASSIC.addon.v1.3.1.zip"
projectURL="https://github.com/BEAST2-Dev/beast-classic/"
description="BEAST classes ported from BEAST 1 in wrappers" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.4.0'/>
</package>
<package name='BEAST_CLASSIC' version='1.3.2'
url="https://github.com/BEAST2-Dev/beast-classic/releases/download/v1.3.0/BEAST_CLASSIC.addon.v1.3.2.zip"
projectURL="https://github.com/BEAST2-Dev/beast-classic/"
description="BEAST classes ported from BEAST 1 in wrappers" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.4.0'/>
</package>
<package name='GEO_SPHERE' version='0.2.0'
url="https://github.com/BEAST2-Dev/beast-geo/releases/download/v0.2.0/GEO_SPHERE.addon.v0.2.0.zip"
projectURL="https://github.com/BEAST2-Dev/beast-geo/"
description="Whole world phylogeography" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.4.0' atmost='1.4.0'/>
</package>
<package name='GEO_SPHERE' version='1.0.0'
url="https://github.com/BEAST2-Dev/beast-geo/releases/download/v1.0.0/GEO_SPHERE.addon.v1.0.0.zip"
projectURL="https://github.com/BEAST2-Dev/beast-geo/"
description="Whole world phylogeography" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.5.3'/>
</package>
<package name='GEO_SPHERE' version='1.1.1'
url="https://github.com/BEAST2-Dev/beast-geo/releases/download/v1.1.0/GEO_SPHERE.addon.v1.1.1.zip"
description="Whole world phylogeography"
projectURL="https://github.com/BEAST2-Dev/beast-geo">
<depends on='beast2' atleast='2.4.3'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
</package>
<package name='GEO_SPHERE' version='1.1.2'
url="https://github.com/BEAST2-Dev/beast-geo/releases/download/v1.1.0/GEO_SPHERE.addon.v1.1.2.zip"
description="Whole world phylogeography"
projectURL="https://github.com/BEAST2-Dev/beast-geo">
<depends on='beast2' atleast='2.4.3'/>
<depends on='BEASTLabs' atleast='1.6.0'/>
</package>
<package name='CA' version='1.2.1'
url="https://github.com/BEAST2-Dev/cladeage/releases/download/v1.2.0/CA.addon.v1.2.1.zip"
projectURL="https://github.com/BEAST2-Dev/cladeage/"
description="CladeAge aPackage for fossil calibrations">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='MASTER' version='5.0.2'
url="https://github.com/tgvaughan/MASTER/releases/download/v5.0.2/MASTER.package.v5.0.2.zip"
description="Stochastic population dynamics simulation"
projectURL="http://tgvaughan.github.io/MASTER" >
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='MASTER' version='5.1.0'
url="https://github.com/tgvaughan/MASTER/releases/download/v5.1.0/MASTER.package.v5.1.0.zip"
description="Stochastic population dynamics simulation"
projectURL="http://tgvaughan.github.io/MASTER" >
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='MASTER' version='5.1.1'
url="https://github.com/tgvaughan/MASTER/releases/download/v5.1.1/MASTER.package.v5.1.1.zip"
description="Stochastic population dynamics simulation"
projectURL="http://tgvaughan.github.io/MASTER" >
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='MultiTypeTree' version='6.2.1'
url="https://github.com/tgvaughan/MultiTypeTree/releases/download/v6.2.1/MultiTypeTree.v6.2.1.zip"
description="Structured coalescent inference"
projectURL="http://tgvaughan.github.io/MultiTypeTree" >
<depends on='BEAST' atleast='2.4.0' />
</package>
<package name='MultiTypeTree' version='6.3.0'
url="https://github.com/tgvaughan/MultiTypeTree/releases/download/v6.3.0/MultiTypeTree.v6.3.0.zip"
description="Structured coalescent inference"
projectURL="http://tgvaughan.github.io/MultiTypeTree" >
<depends on='BEAST' atleast='2.4.0' />
</package>
<package name='MultiTypeTree' version='6.3.1'
url="https://github.com/tgvaughan/MultiTypeTree/releases/download/v6.3.1/MultiTypeTree.v6.3.1.zip"
description="Structured coalescent inference"
projectURL="http://tgvaughan.github.io/MultiTypeTree" >
<depends on='BEAST' atleast='2.4.0' />
</package>
<package name='bacter' version='1.2.1'
url="https://github.com/tgvaughan/bacter/releases/download/v1.2.1/bacter.v1.2.1.zip"
description="Bacterial ARG inference."
projectURL="http://tgvaughan.github.io/bacter" >
<depends on='BEAST' atleast='2.4'/>
</package>
<package name='bacter' version='1.2.2'
url="https://github.com/tgvaughan/bacter/releases/download/v1.2.2/bacter.v1.2.2.zip"
description="Bacterial ARG inference."
projectURL="http://tgvaughan.github.io/bacter" >
<depends on='BEAST' atleast='2.4'/>
</package>
<package name='bacter' version='1.2.3'
url="https://github.com/tgvaughan/bacter/releases/download/v1.2.3/bacter.v1.2.3.zip"
description="Bacterial ARG inference."
projectURL="http://tgvaughan.github.io/bacter" >
<depends on='BEAST' atleast='2.4'/>
</package>
<package name='EpiInf' version='5.0.1'
url="https://github.com/tgvaughan/epiinf/releases/download/v5.0.1/EpiInf.v5.0.1.zip"
description="BD/SIR/SIS epidemic trajectory inference."
projectURL="http://tgvaughan.github.io/EpiInf" >
<depends on='BEAST' atleast='2.4'/>
<depends on='SA' atleast='1.1.5'/>
</package>
<package name='EpiInf' version='6.0.0'
url="https://github.com/tgvaughan/epiinf/releases/download/v6.0.0/EpiInf.v6.0.0.zip"
description="BD/SIR/SIS epidemic trajectory inference."
projectURL="http://tgvaughan.github.io/EpiInf" >
<depends on='BEAST' atleast='2.4'/>
<depends on='SA' atleast='1.1.5'/>
</package>
<!-- DISSECT is retired
<package name='DISSECT' version='1.2.0'
url="http://www.indriid.com/2015/DISSECT.addon.v1.2.0.zip"
description="Species delimitation with *BEAST">
<depends on='beast2' atleast='2.3.0'/>
</package>
-->
<package name='STACEY' version='1.2.2'
url="http://www.indriid.com/2016/STACEY.addon.v1.2.2.zip"
projectURL="http://www.indriid.com"
description="Species delimitation and species tree estimation">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='STACEY' version='1.2.3'
url="http://indriid.com/2017/STACEY.addon.v1.2.3.zip"
projectURL="http://www.indriid.com"
description="Species delimitation and species tree estimation">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='STACEY' version='1.2.4'
url="http://indriid.com/2017/STACEY.addon.v1.2.4.zip"
description="Species delimitation and species tree estimation"
projectURL="http://indriid.com/software.html">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='DENIM' version='0.3.0'
url="http://indriid.com/2017/DENIM.addon.v0.3.0.zip"
description="Divergence Estimation Notwithstanding ILS and Migration"
projectURL="http://indriid.com/software.html">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='DENIM' version='0.3.1'
url="http://indriid.com/2018/DENIM.addon.v0.3.1.zip"
description="Divergence Estimation Notwithstanding ILS and Migration"
projectURL="http://indriid.com/software.html">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name="MODEL_SELECTION" version="1.2.0"
url="https://github.com/BEAST2-Dev/model-selection/releases/download/v1.2.0/MODEL_SELECTION.addon.v1.2.0.zip"
projectURL="https://github.com/BEAST2-Dev/model-selection"
description="Select models through path sampling/stepping stone analysis">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name="MODEL_SELECTION" version="1.3.1"
url="https://github.com/BEAST2-Dev/model-selection/releases/download/v1.3.0/MODEL_SELECTION.addon.v1.3.1.zip"
projectURL="https://github.com/BEAST2-Dev/model-selection"
description="Select models through path sampling/stepping stone analysis">
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.5.0'/>
</package>
<package name="MODEL_SELECTION" version="1.3.4"
url="https://github.com/BEAST2-Dev/model-selection/releases/download/v1.3.0/MODEL_SELECTION.addon.v1.3.4.zip"
description="Select models through path sampling/stepping stone analysis"
projectURL="https://github.com/BEAST2-Dev/model-selection">
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.5.3'/>
</package>
<package name='phylodynamics' version='1.2.0'
url="https://github.com/BEAST2-Dev/phylodynamics/releases/download/1.2.0/phylodynamics.addon.1.2.0.zip"
projectURL="https://github.com/BEAST2-Dev/phylodynamics"
description="BDSIR and Stochastic Coalescent" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BDSKY' atleast='1.3.0' atmost='1.3.2'/>
</package>
<package name='phylodynamics' version='1.2.1'
url="https://github.com/BEAST2-Dev/phylodynamics/releases/download/1.2.0/phylodynamics.addon.1.2.1.zip"
projectURL="https://github.com/BEAST2-Dev/phylodynamics"
description="BDSIR and Stochastic Coalescent" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BDSKY' atleast='1.3.3'/>
</package>
<package name='bdmm' version='0.2.0'
url="https://github.com/denisekuehnert/bdmm/releases/download/0.2.0/BDMM.addon.0.2.0.zip"
description="pre-release of multitype birth-death model (aka birth-death-migration model)"
projectURL="https://github.com/denisekuehnert/bdmm" >
<depends on='beast2' atleast='2.4.4'/>
<depends on='MultiTypeTree' atleast='6.0.0'/>
</package>
<package name='RBS' version='1.3.1'
url="https://github.com/BEAST2-Dev/rb-beast/releases/download/v1.3.0/RBS.addon.v1.3.1.zip"
projectURL="https://github.com/BEAST2-Dev/rb-beast"
description="Reversible-jump Based substitution model" >
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='SA' version='1.1.4'
url="https://github.com/CompEvol/sampled-ancestors/releases/download/v1.1.4/SA.addon.v1.1.4.zip"
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees" >
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='SA' version='1.1.5'
url="https://github.com/CompEvol/sampled-ancestors/releases/download/v1.1.4/SA.addon.v1.1.5.zip"
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.5.3'/>
</package>
<package name='SA' version='1.1.6'
url="https://github.com/CompEvol/sampled-ancestors/releases/download/v1.1.6/SA.addon.v1.1.6.zip"
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.5.3'/>
</package>
<package name='SA' version='1.1.7'
url="https://github.com/CompEvol/sampled-ancestors/releases/download/v1.1.7/SA.addon.v1.1.7.zip"
projectURL="https://github.com/CompEvol/sampled-ancestors"
description="Sampled ancestor trees" >
<depends on='beast2' atleast='2.4.0'/>
<depends on='BEASTLabs' atleast='1.5.3'/>
</package>
<package name='SNAPP' version='1.3.0'
url="https://github.com/BEAST2-Dev/SNAPP/releases/download/v1.3.0/SNAPP.addon.v1.3.0.zip"
description="SNP and AFLP Phylogenies"
projectURL="http://beast2.org/snapp/">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name="substBMA" version="1.2.2"
url="https://github.com/jessiewu/substBMA/releases/download/v1.2.2/substBMA.v1.2.2.zip"
projectURL="https://github.com/jessiewu/substBMA"
description="Substitution Bayesian Model Averaging">
<depends on="BEAST" atleast="2.4.0" atmost="2.4.4"/>
</package>
<package name='BEASTShell' version='1.3.0'
url="https://github.com/CompEvol/beastshell/releases/download/v1.3.0/BEASTShell.addon.v1.3.0.zip"
projectURL="https://github.com/CompEvol/beastshell"
description="BEAST Shell - BeanShell scripting for BEAST">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='MM' version='1.0.4'
url="https://github.com/CompEvol/morph-models/releases/download/1.0.4/MM.addon.v1.0.4.zip"
projectURL="https://github.com/CompEvol/morph-models"
description="Enables models of morphological character evolution">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='MM' version='1.0.5'
url="https://github.com/CompEvol/morph-models/releases/download/1.0.5/MM.addon.v1.0.5.zip"
projectURL="https://github.com/CompEvol/morph-models"
description="Enables models of morphological chatacter evolution">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='MGSM' version='0.2.1'
url="https://github.com/BEAST2-Dev/MGSM/releases/download/v0.2.0/MGSM.addon.v0.2.1.zip"
description="Multi-gamma and relaxed gamma site models"
projectURL="https://github.com/BEAST2-Dev/MGSM/wiki">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='bModelTest' version='0.2.0'
url="https://github.com/BEAST2-Dev/bModelTest/releases/download/v0.2.0/bModelTest.addon.v0.2.0.zip"
projectURL="https://github.com/BEAST2-Dev/bModelTest/wiki"
description="Bayesian model test for nucleotide subst models, gamma rate heterogeneity and invariant sites">
<depends on='beast2' atleast='2.4.0'/>
</package>
<package name='bModelTest' version='1.0.0'
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