CBAN/packages-extra-2.7.xml at master · CompEvol/CBAN · GitHub

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<!-- Extra package file for v2.7.X packages -->

<!-- Suitable for packages that are not peer-reviewed   -->
<!-- Peer reviewed packages can go in packages2.7.xml   -->

<packages>
    <package name="AlmostDistributions" version="0.2.0"
        url="https://github.com/rbouckaert/AlmostDistributions/releases/download/v0.2.0/AlmostDistributions.addon.v0.2.0.zip"
        description="Almost-distributions"
        projectURL="https://github.com/rbouckaert/AlmostDistributions">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEASTLabs' atleast='2.0.0'/>
    </package>
    <package name="AlmostDistributions" version="0.2.1"
        url="https://github.com/rbouckaert/AlmostDistributions/releases/download/v0.2.0/AlmostDistributions.package.v0.2.1.zip"
        description="Almost-distributions"
        projectURL="https://github.com/rbouckaert/AlmostDistributions">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEASTLabs' atleast='2.0.0'/>
    </package>

    <package name="Experimenter" version="0.2.0"
        url="https://github.com/christiaanjs/beast-validation/releases/download/v0.2.0/Experimenter.addon.v0.2.0.zip"
        description="Experimenter"
        projectURL="https://github.com/christiaanjs/beast-validation/">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
        <depends on='BEASTLabs' atleast='2.0.0'/>
    </package>


    <package name="IndelDollo" version="0.0.1"
        url="https://github.com/jordandouglas/IndelDollo/releases/download/0.0.1/IndelDollo.addon.v0.0.1.zip"
        description="Mutations, insertions, and deletions"
        projectURL="https://github.com/jordandouglas/IndelDollo/">
        <depends on='BEAST.base' atleast='2.7.3'/>
        <depends on='BEAST.app' atleast='2.7.3'/>
    </package>

    <package name="CorrelatedTrait" version="0.0.5"
        url="https://github.com/rbouckaert/CorrelatedTrait/releases/download/v0.0.5/CorrelatedTrait.package.v0.0.5.zip"
        description="Analysis for a fixed tree or fixed tree set"
        projectURL="https://github.com/rbouckaert/CorrelatedTrait">
        <depends on='BEAST.base' atleast='2.7.4'/>
        <depends on='BEAST.app' atleast='2.7.4'/>
        <depends on='BEASTLabs' atleast='2.0.0'/>
        <depends on='BEAST_CLASSIC' atleast='1.6.1'/>
        <depends on='Babel' atleast='0.4.1'/>
    </package>

    <package name='HetMM' version='0.0.1'
           url="https://github.com/jordandouglas/HetMM/releases/download/v0.0.1/HetMM.addon.v0.0.1.zip"
           description="Heterogeneous Michaelis-Menten model"
           projectURL="https://github.com/jordandouglas/HetMM">
        <depends on='BEAST.base' atleast='2.7.5'/>
        <depends on='BEAST.app' atleast='2.7.5'/>
    </package>

    <package name='beastmap' version='0.0.3'
           url="https://github.com/jordandouglas/BeastMap/releases/download/v0.0.3/beastmap.package.v0.0.3.zip"
           description="Stochastic mapping and ancestral sequence/state reconstruction"
           projectURL="https://github.com/jordandouglas/BeastMap/">
        <depends on='BEAST.base' atleast='2.7.8'/>
        <depends on='BEAST.app' atleast='2.7.8'/>
        <depends on='CodonSubstModels' atleast='2.0.1'/>
        <depends on='starbeast3' atleast='1.2.1'/>
        <depends on='MM' atleast='1.2.0'/>
    </package>


    <package name='FoldBeast' version='0.0.1'
           url="https://github.com/jordandouglas/FoldBeast/releases/download/v0.0.1/FoldBeast.package.v0.0.1.zip"
           description="3Di characters in phylogenetics"
           projectURL="https://github.com/jordandouglas/FoldBeast/">
        <depends on='BEAST.base' atleast='2.7.5'/>
        <depends on='BEAST.app' atleast='2.7.5'/>
        <depends on='bModelTest' atleast='1.3.0'/>
        <depends on='OBAMA' atleast='1.1.1'/>
    </package>


    <package name='FoldBeast' version='0.0.2'
           url="https://github.com/jordandouglas/FoldBeast/releases/download/v0.0.2/FoldBeast.package.v0.0.2.zip"
           description="3Di characters in phylogenetics"
           projectURL="https://github.com/jordandouglas/FoldBeast/">
        <depends on='BEAST.base' atleast='2.7.7'/>
        <depends on='BEAST.app' atleast='2.7.7'/>
        <depends on='bModelTest' atleast='1.3.0'/>
        <depends on='OBAMA' atleast='1.1.1'/>
    </package>


    <package name='gammaspike' version='0.0.1'
           url="https://github.com/jordandouglas/GammaSpikeModel/releases/download/v0.0.1/gammaspike.package.v0.0.1.zip"
           description="A punctuated equilibrium clock model"
           projectURL="https://github.com/jordandouglas/GammaSpikeModel">
        <depends on='BEAST.base' atleast='2.7.7'/>
        <depends on='BEAST.app' atleast='2.7.7'/>
        <depends on='SA' atleast='2.1.1'/>
    </package>

    <package name='gammaspike' version='0.0.2'
           url="https://github.com/jordandouglas/GammaSpikeModel/releases/download/v0.0.2/gammaspike.package.v0.0.2.zip"
           description="A punctuated equilibrium clock model"
           projectURL="https://github.com/jordandouglas/GammaSpikeModel">
        <depends on='BEAST.base' atleast='2.7.7'/>
        <depends on='BEAST.app' atleast='2.7.7'/>
        <depends on='SA' atleast='2.1.1'/>
    </package>

    <package name='gammaspike' version='0.0.3'
           url="https://github.com/jordandouglas/GammaSpikeModel/releases/download/v0.0.3/gammaspike.package.v0.0.3.zip"
           description="A punctuated equilibrium clock model"
           projectURL="https://github.com/jordandouglas/GammaSpikeModel">
        <depends on='BEAST.base' atleast='2.7.7'/>
        <depends on='BEAST.app' atleast='2.7.7'/>
        <depends on='SA' atleast='2.1.1'/>
    </package>

    <package name="MultiTypeSpikeModel" version="1.0.1"
             url="https://github.com/EwanCiuffi/MultiTypeSpikeModel/releases/download/v1.0.1/MultiTypeSpikeModel.package.v1.0.1.zip"
             projectURL="https://github.com/EwanCiuffi/MultiTypeSpikeModel"
             description="Clock model with trait-dependent bursts of change at branching events">
        <depends on="BEAST.base" atleast="2.7.5" atmost="2.7.9"/>
        <depends on="SA" atleast="2.1.1"/>
        <depends on="BDMM-Prime" atleast="2.2.2"/>
    </package>

    <package name="MultiTypeSpikeModel" version="1.0.2"
             url="https://github.com/EwanCiuffi/MultiTypeSpikeModel/releases/download/v1.0.2/MultiTypeSpikeModel.package.v1.0.2.zip"
             projectURL="https://github.com/EwanCiuffi/MultiTypeSpikeModel"
             description="Clock model with trait-dependent bursts of change at branching events">
        <depends on="BEAST.base" atleast="2.7.5" atmost="2.7.9"/>
        <depends on="SA" atleast="2.1.1"/>
        <depends on="BDMM-Prime" atleast="2.2.2"/>
    </package>

    <package name='resub' version='0.0.1'
           url="https://github.com/jordandouglas/resub/releases/download/v0.0.1/resub.package.v0.0.1.zip"
           description="Refinement expansion substitution model"
           projectURL="https://github.com/jordandouglas/resub">
        <depends on='BEAST.base' atleast='2.7.7'/>
        <depends on='BEAST.app' atleast='2.7.7'/>
    </package>

    <package name="CCD" version="0.0.4"
	     url="https://github.com/CompEvol/CCD/releases/download/v0.0.1/CCD.package.v0.0.4.zip"
	     projectURL="https://github.com/CompEvol/CCD"
	     description="Sensible tree set summary/point estimates.">
        <depends on='BEAST.base' atleast='2.7.6'/>
        <depends on='BEAST.app' atleast='2.7.6'/>
    </package>


    <package name="BREATH" version="0.0.5"
	     url="https://github.com/rbouckaert/transmission/releases/download/v0.0.5/BREATH.v0.0.5.zip"
	     projectURL="https://github.com/rbouckaert/transmission"
	     description="Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories">
        <depends on='BEAST.base' atleast='2.7.6'/>
        <depends on='BEAST.app' atleast='2.7.6'/>
    </package>
    <package name="BREATH" version="0.0.6"
	     url="https://github.com/rbouckaert/transmission/releases/download/v0.0.6/BREATH.v0.0.6.zip"
	     projectURL="https://github.com/rbouckaert/transmission"
	     description="Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories">
        <depends on='BEAST.base' atleast='2.7.6'/>
        <depends on='BEAST.app' atleast='2.7.6'/>
    </package>
    <package name="BREATH" version="0.0.7"
	     url="https://github.com/rbouckaert/transmission/releases/download/v0.0.7/BREATH.v0.0.7.zip"
	     projectURL="https://github.com/rbouckaert/transmission"
	     description="Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories">
        <depends on='BEAST.base' atleast='2.7.6'/>
        <depends on='BEAST.app' atleast='2.7.6'/>
    </package>

    <package name="5rf" version="0.0.1"
	     url="https://github.com/rbouckaert/5rf/releases/download/v0.0.1/5rf.package.v0.0.1.zip"
	     projectURL="https://github.com/rbouckaert/5rf/"
	     description="Rate Class Root Frequency Model">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
    </package>
    <package name="5rf" version="0.0.2"
	     url="https://github.com/rbouckaert/5rf/releases/download/v0.0.1/5rf.package.v0.0.2.zip"
	     projectURL="https://github.com/rbouckaert/5rf/"
	     description="Rate Class Root Frequency Model">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
    </package>

    <package name="RBS" version="1.5.0"
	     url="https://github.com/BEAST2-Dev/rb-beast/releases/download/v1.5.0/RBS.package.v1.5.0.zip"
	     projectURL="https://github.com/BEAST2-Dev/rb-beast/"
	     description="AutoPartition and Reverisble Jump Based substitution model">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
    </package>
    <package name="RBS" version="1.5.1"
	     url="https://github.com/BEAST2-Dev/rb-beast/releases/download/v1.5.0/RBS.package.v1.5.1.zip"
	     projectURL="https://github.com/BEAST2-Dev/rb-beast/"
	     description="AutoPartition and Reverisble Jump Based substitution model">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
    </package>
    <package name="RBS" version="1.5.2"
	     url="https://github.com/BEAST2-Dev/rb-beast/releases/download/v1.5.0/RBS.package.v1.5.2.zip"
	     projectURL="https://github.com/BEAST2-Dev/rb-beast/"
	     description="AutoPartition and Reverisble Jump Based substitution model">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
    </package>

    <package name="rootfreqs" version="0.0.2"
	     url="https://github.com/rbouckaert/rootfreqs/releases/download/v0.0.2/rootfreqs.package.v0.0.2.zip"
	     projectURL="https://github.com/rbouckaert/rootfreqs"
	     description="Allows root frequencies to be specified per site.">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
    </package>

    <package name="EpochClockModel" version="0.0.2"
	     url="https://github.com/rbouckaert/EpochClockModel/releases/download/v0.0.2/EpochClockModel.v0.0.2.zip"
	     projectURL="https://github.com/rbouckaert/EpochClockModel"
	     description="Add clock models that have different mean rates at different epochs">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
    </package>

	<package name="TyCHE" version="0.0.3"
         url="https://github.com/hoehnlab/tyche/releases/download/v0.0.3/TyCHE.v0.0.3.zip"
         projectURL="https://tyche.readthedocs.io"
         description="Type-linked Clocks for Heterogenous Evolution">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
		<depends on='BEAST_CLASSIC' atleast='1.6.3'/>
    </package>
	<package name="TyCHE" version="0.0.10"
         url="https://github.com/hoehnlab/tyche/releases/download/v0.0.10/TyCHE.v0.0.10.zip"
         projectURL="https://tyche.readthedocs.io"
         description="Type-linked Clocks for Heterogenous Evolution">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
		<depends on='BEAST_CLASSIC' atleast='1.6.3'/>
    </package>
	<package name="TyCHE" version="0.0.11"
         url="https://github.com/hoehnlab/tyche/releases/download/v0.0.11/TyCHE.v0.0.11.zip"
         projectURL="https://tyche.readthedocs.io"
         description="Type-linked Clocks for Heterogenous Evolution">
        <depends on='BEAST.base' atleast='2.7.0'/>
        <depends on='BEAST.app' atleast='2.7.0'/>
		<depends on='BEAST_CLASSIC' atleast='1.6.3'/>
    </package>


    <package name="TargetedBeast" version="2.2.0"
         url="https://github.com/nicfel/targetedbeast/releases/download/v2.2.0/TargetedBeast.v2.2.0.zip"
         projectURL="https://github.com/nicfel/targetedbeast/"
         description="Targeted MCMC operators for Improving the Scalability of Bayesian Phylodynamic Inference">
        <depends on='BEAST.base' atleast='2.7.2'/>
        <depends on='BEAST.app' atleast='2.7.2'/>
    </package>

    <package name="BEAST2Lang" version="0.0.1"
         url="https://github.com/CompEvol/beast2lang/releases/download/0.0.1/BEAST2Lang.v0.0.1.zip"
         projectURL="https://github.com/CompEvol/beast2lang/"
         description="Run a Beast2 model using the definition language">
		<depends on='BEAST.base' atleast='2.7.8'/>
		<depends on='BEAST.app' atleast='2.7.8'/>
		<depends on='BEASTLabs' atleast='2.0.3'/>
    </package>

	<package name='BEASTBooster' version='0.0.2'
             description="BEAST Booster"
             projectURL="https://github.com/rbouckaert/beastbooster"
             url="https://github.com/rbouckaert/beastbooster/releases/download/v0.0.2/BEASTBooster.v0.0.2.zip">
		<depends on='BEAST.base' atleast='2.7.8'/>
		<depends on='BEAST.app' atleast='2.7.8'/>
		<depends on='BEASTLabs' atleast='2.0.3'/>
	</package>

	<package name='online' version='0.0.2'
             description="Online and faster parallel phylogenetics"
             projectURL="https://github.com/rbouckaert/online"
             url="https://github.com/rbouckaert/online/releases/download/v0.0.2/online.package.v0.0.2.zip">
		<depends on='BEAST.base' atleast='2.7.8'/>
		<depends on='BEAST.app' atleast='2.7.8'/>
		<depends on='BEASTLabs' atleast='2.0.3'/>
		<depends on='BEASTBooster' atleast='0.0.2'/>
	</package>

	<package name='PhyloPotts' version='0.0.1'
             description="PhyloPotts model"
             projectURL="https://github.com/rbouckaert/potts"
             url="https://github.com/rbouckaert/potts/releases/download/v0.0.1/PhyloPotts.v0.0.1.zip">
		<depends on='BEAST.base' atleast='2.7.0'/>
		<depends on='BEAST.app' atleast='2.7.0'/>
	</package>

	<package name='MixedEffectsClock' version='0.1.1'
             description="Mixed-effects molecular clock models."
             projectURL="https://github.com/sebastianduchene/MixedEffectsClock"
             url="https://github.com/sebastianduchene/MixedEffectsClock/releases/download/v0.1.1/MixedEffectsClock.v0.1.1.zip">
		<depends on='BEAST.base' atleast='2.7.7'/>
	</package>

</packages>