CBAN/packages2.8.xml at master · CompEvol/CBAN · GitHub

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<!-- BEAST 2.8 package repository: live alpha testing of the full new framework -->
<packages>
    <package name="MM" version="1.3.1"
        url="https://github.com/CompEvol/morph-models/releases/download/v1.3.1-beta1/MM.v1.3.1.zip"
        projectURL="https://github.com/CompEvol/morph-models"
        description="Lewis MK and MKv substitution models for discrete morphological data">
        <depends on="BEAST.base" atleast="2.8.0"/>
    </package>
    <package name="SA" version="2.3.0"
        url="https://github.com/CompEvol/sampled-ancestors/releases/download/v2.3.0-beta2/SA.v2.3.0.zip"
        projectURL="https://github.com/CompEvol/sampled-ancestors"
        description="Sampled ancestor trees for BEAST">
        <depends on="BEAST.base" atleast="2.8.0"/>
    </package>
    <package name="BEASTLabs" version="2.1.1"
        url="https://github.com/BEAST2-Dev/BEASTLabs/releases/download/v2.1.1/BEASTLabs.v2.1.1.zip"
        projectURL="https://github.com/BEAST2-Dev/BEASTLabs"
        description="BEAST Labs utility library">
        <depends on="BEAST.base" atleast="2.8.0"/>
    </package>
    <package name='ORC' version='1.3.0'
                url="https://github.com/jordandouglas/ORC/releases/download/v1.3.0/ORC.v1.3.0.zip"
                description="Optimised Relaxed Clock model"
                projectURL="https://github.com/jordandouglas/ORC/">
        <depends on='BEAST.base' atleast='2.8.0'/>
    </package>
    <package name='ORC' version='1.3.1'
                url="https://github.com/jordandouglas/ORC/releases/download/v1.3.1/ORC.v1.3.1.zip"
                description="Optimised Relaxed Clock model"
                projectURL="https://github.com/jordandouglas/ORC/">
        <depends on='BEAST.base' atleast='2.8.0'/>
    </package>
    <package name='gammaspike' version='1.3.0'
           url="https://github.com/jordandouglas/GammaSpikeModel/releases/download/v1.3.0/gammaspike.v1.3.0.zip"
           description="A clock model that captures and tests for punctuated evolution"
           projectURL="https://github.com/jordandouglas/GammaSpikeModel">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
        <depends on='SA' atleast='2.3.0'/>
        <depends on='ORC' atleast='1.3.0'/>
    </package>
     <package name='starbeast3' version='1.3.0'
            url="https://github.com/rbouckaert/starbeast3/releases/download/v1.3.0/starbeast3.v1.3.0.zip"
            description="StarBeast3 multispecies coalescent using advanced MCMC operators"
             projectURL="https://github.com/rbouckaert/starbeast3">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
        <depends on='SA' atleast='2.3.0'/>
        <depends on='ORC' atleast='1.3.1'/>
    </package>
    <package name='speedemon' version='1.2.0'
            url="https://github.com/rbouckaert/speedemon/releases/download/v1.2.0/speedemon.v1.2.0.zip"
            description="Fast species delimitation under the multispecies coalescent"
             projectURL="https://github.com/rbouckaert/speedemon">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
    </package>
    <package name="feast" version="11.0.0"
           url="https://github.com/tgvaughan/feast/releases/download/v11.0.0/feast.v11.0.0.zip"
           projectURL="https://tgvaughan.github.io/feast"
           description="Flexible BEAST 2 XML extension package." >
      <depends on="BEAST.base" atleast="2.8.0" atmost="2.8.9"/>
   </package>
    <package name="feast" version="11.0.1"
           url="https://github.com/tgvaughan/feast/releases/download/v11.0.1/feast.v11.0.1.zip"
           projectURL="https://tgvaughan.github.io/feast"
           description="Flexible BEAST 2 XML extension package." >
      <depends on="BEAST.base" atleast="2.8.0" atmost="2.8.9"/>
   </package>
    <package name="ReMASTER" version="3.0.0"
           url="https://github.com/tgvaughan/remaster/releases/download/v3.0.0/remaster.v3.0.0.zip"
           projectURL="https://tgvaughan.github.io/remaster"
           description="Phylodynamic simulation system" >
        <depends on="BEAST.base" atleast="2.8.0" atmost="2.8.9"/>
    </package>
    <package name="ReMASTER" version="3.0.1"
           url="https://github.com/tgvaughan/remaster/releases/download/v3.0.1/remaster.v3.0.1.zip"
           projectURL="https://tgvaughan.github.io/remaster"
           description="Phylodynamic simulation system" >
        <depends on="BEAST.base" atleast="2.8.0" atmost="2.8.9"/>
    </package>
    <package name="BDMM-Prime" version="3.0.0"
           url="https://github.com/tgvaughan/BDMM-Prime/releases/download/v3.0.0/BDMM-Prime.v3.0.0.zip"
           projectURL="https://tgvaughan.github.io/BDMM-Prime"
           description="Linear birth-death phylodynamics">
        <depends on="BEAST.base" atleast="2.8.0" atmost="2.8.9"/>
        <depends on="BEAST.app" atleast="2.8.0" atmost="2.8.9"/>
        <depends on="SA" atleast="2.3.0"/>
    </package>
    <package name="BEAST_CLASSIC" version="1.7.1"
        url="https://github.com/BEAST2-Dev/beast-classic/releases/download/v1.7.1/BEAST_CLASSIC.v1.7.1.zip"
        projectURL="https://github.com/BEAST2-Dev/beast-classic"
        description="Classic BEAST models: phylogeography, GMRF skyride, GLM">
        <depends on="BEAST.base" atleast="2.8.0"/>
    </package>
    <package name="Mascot" version="3.1.0"
        url="https://github.com/CompEvol/Mascot/releases/download/v3.1.0-beta1/Mascot.v3.1.0.zip"
        projectURL="https://github.com/CompEvol/Mascot"
        description="Marginal approximation of the structured coalescent">
        <depends on="BEAST.base" atleast="2.8.0"/>
    </package>
    <package name="CoupledMCMC" version="1.3.0"
        url="https://github.com/CompEvol/CoupledMCMC/releases/download/v1.3.0-beta1/CoupledMCMC.v1.3.0.zip"
        projectURL="https://github.com/CompEvol/CoupledMCMC"
        description="Coupled MCMC (MC3) for BEAST">
        <depends on="BEAST.base" atleast="2.8.0"/>
    </package>
    <package name='SSM' version='1.3.1'
        url="https://github.com/BEAST2-Dev/substmodels/releases/download/v1.3.0/SSM.v1.3.1.zip"
        description="Standard Nucleotide Substitution Models"
        projectURL="https://github.com/BEAST2-Dev/substmodels/">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
    </package>
    <package name='BICEPS' version='1.2.0'
                url="https://github.com/rbouckaert/biceps/releases/download/v1.2.0/BICEPS.v1.2.0.zip"
                description="Bayesian Integrated Coalescent Epoch PlotS + Yule Skyline"
                projectURL="https://github.com/rbouckaert/biceps/">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
    </package>
    <package name="contacTrees" version="2.0.0"
                url="https://github.com/NicoNeureiter/contacTrees/releases/download/v2.0.0/contacTrees.v2.0.0.zip"
                projectURL="https://github.com/NicoNeureiter/contacTrees"
                description="Phylogenetic model for language evolution with horizontal transfer">
        <depends on="BEAST.base" atleast="2.8.0" atmost="2.8.9"/>
        <depends on="BEAST.app" atleast="2.8.0" atmost="2.8.9"/>
    </package>
    <package name='bModelTest' version='1.4.0'
        url="https://github.com/BEAST2-Dev/bModelTest/releases/download/v1.4.0/BMT.v1.4.0.zip"
        description="Bayesian model test: site model averaging and selection for BEAST 3"
        projectURL="https://github.com/BEAST2-Dev/bModelTest/">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
    </package>
    <package name='CCD' version='1.2.2'
        url="https://github.com/CompEvol/CCD/releases/download/v1.2.2/CCD.v1.2.2.zip"
        description="Conditional Clade Distribution methods for BEAST 3"
        projectURL="https://github.com/CompEvol/CCD/">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
    </package>
    <package name='MODEL_SELECTION' version='1.7.0'
        url="https://github.com/BEAST2-Dev/model-selection/releases/download/v1.7.0/MODEL_SELECTION.v1.7.0.zip"
        description="Select models through path sampling/stepping stone analysis"
        projectURL="https://github.com/BEAST2-Dev/model-selection/">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
    </package>
    <package name='NS' version='1.3.1'
        url="https://github.com/BEAST2-Dev/nested-sampling/releases/download/v1.3.1/NS.v1.3.1.zip"
        description="BEAST 3 package for Nested Sampling"
        projectURL="https://github.com/BEAST2-Dev/nested-sampling/">
        <depends on='BEAST.base' atleast='2.8.0'/>
        <depends on='BEAST.app' atleast='2.8.0'/>
        <depends on='MODEL_SELECTION' atleast='1.7.0'/>
    </package>
    <package name="tidetree" version="2.0.0"
	     url="https://github.com/seidels/tidetree/releases/download/v2.0.0/tidetree.v2.0.0.zip"
	     projectURL="https://github.com/seidels/tidetree"
	     description="Estimating single-cell trees from lineage tracing data">
      <depends on="BEAST.base" atleast="2.8.0"/>
      <depends on="feast" atleast="11.0.1"/>
    </package>
<!--  https://doi.org/10.1093/molbev/msag080    -->
    <package name="ADB" version="0.1.0"
        url="https://github.com/pilarskj/ADB/releases/download/v0.1.0/ADB.v0.1.0.zip"
        projectURL="https://github.com/pilarskj/ADB"
        description="Age-dependent branching model for phylodynamic inference">
        <depends on="BEAST.base" atleast="2.8.0"/>
    </package>
</packages>