XML reference for BEAST 2?

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Santiago Sánchez

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Sep 8, 2014, 3:22:16 PM9/8/14

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Dear Remco,

I was wondering if there is an XML reference for BEAST 2 available. I know there was one for BEAST 1.x on the wiki. I can't seem to find it (if there is one) on the BEAST2 website.

Thanks,

Santiago

--
Santiago Sánchez-Ramírez

Department of Ecology and Evolutionary Biology, University of Toronto

Department of Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

Other email: santiago...@mail.utoronto.ca

Tel. 416-586-8025

Remco Bouckaert

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Sep 9, 2014, 1:42:12 AM9/9/14

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Dear Santiago,

When you run from a terminal

java -cp /path/to/beast.jar beast.app.DocMaker

a set of HTML pages will be created in the /tmp directory. If you open /tmp/index.html in a web-browser you can navigate from there to any of the classes/XML elements. Every page lists a set of inputs, which translate directly to XML attribute names.

If you have packages installed these packages will be documented as well.

Cheers,

Remco

Nick Matzke

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Feb 2, 2015, 4:17:25 PM2/2/15

to beast...@googlegroups.com

Hi all,

I have just installed Beast2.2.0 from the .dmg on the Beast2 website. I would like to get the HTML documentation of each XML element, which is quite handy.

However, this documentation command doesn't seem to work in this version. I am using Mac OS X 10.9, latest Java.

Here's the error message:

============================

java -cp /Applications/BEAST_2.2.0/lib/beast.jar beast.app.DocMaker

Exception in thread "main" java.lang.UnsupportedClassVersionError: beast/app/DocMaker : Unsupported major.minor version 52.0

at java.lang.ClassLoader.defineClass1(Native Method)

at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)

at java.lang.ClassLoader.defineClass(ClassLoader.java:621)

at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)

at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)

at java.net.URLClassLoader.access$000(URLClassLoader.java:58)

at java.net.URLClassLoader$1.run(URLClassLoader.java:197)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

============================

Cheers!

Nick

Remco Bouckaert

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Feb 2, 2015, 7:03:02 PM2/2/15

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Hi Nick,

The error message you get indicate that the java version you use is not compatible with the java version required by BEAST 2.2.0, which is java 8.

If you run “java -version” from the command line, it should report something like

java version "1.8.0_11"

Java(TM) SE Runtime Environment (build 1.8.0_11-b12)

Java HotSpot(TM) 64-Bit Server VM (build 25.11-b03, mixed mode)

You may need to change the default Java version (or set the full path to where you have Java 8 installed) to get DocMaker to run.

Cheers,

Remco

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Nick Matzke

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Feb 3, 2015, 12:11:19 PM2/3/15

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Thanks for this hint Remco!

So after fiddling around a little bit I figured it out. My notes for others:

SHORT VERSION

The easy solution, on my computer at least (which has had several generations of java and who knows what customizations , was to install not just java, but specifically JDK (Java Development Kit). This seemed to update both the java executable, and the associated javac, javadoc, etc., and the necessary symbolic links etc. in /usr/bin/.

Only installing java appeared to only create the java 1.8 executable in a folder at:

/Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java

...and only my browser could see it.

After installing JDK, the Beast2 documentation command worked and Java 1.8 appears to be the default everywhere in my system.

SHORT SHORT VERSION

This worked (updating JDK): http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

This only updated my browser java: https://java.com/en/download/

LONGER (but the JDK install was much easier):

Other handy commands in Terminal:

java -version

javac -version

which java

cd /usr/bin/

ls -l java*

ln -s to change symbolic links

Sorry if this was obvious, but it can be handy to have the obvious stuff google-able.

Cheers!

Nick

Nick Matzke

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Feb 3, 2015, 12:21:25 PM2/3/15

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PS: Not a huge deal from my perspective, but after installing all of the available packages I did get some errors producing some pages (search on "failed"):

====================

java -cp /Applications/BEAST_2.2.0/lib/beast.jar beast.app.DocMaker

Producing documentation...

Probing: BDSSM.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BDSKY/lib/BDSSM.addon.jar

Probing: BEAST_CLASSIC.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BEAST_CLASSIC/lib/BEAST_CLASSIC.addon.jar

Probing: BEASTlabs.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BEASTlabs/lib/BEASTlabs.addon.jar

Probing: autocomplete.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BEASTShell/lib/autocomplete.jar

Probing: BEASTShell.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BEASTShell/lib/BEASTShell.addon.jar

Probing: itextpdf-5.2.1.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BEASTShell/lib/itextpdf-5.2.1.jar

Probing: jtikz.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BEASTShell/lib/jtikz.jar

Probing: rsyntaxtextarea.jar Skip loading file:/Users/matzke/Library/Application Support/BEAST/2.2/BEASTShell/lib/rsyntaxtextarea.jar: contains classs org.fife.io.DocumentReader that is already loaded

Probing: xchart-2.3.3-SNAPSHOT.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/BEASTShell/lib/xchart-2.3.3-SNAPSHOT.jar

Probing: CA.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/CA/lib/CA.addon.jar

Probing: DISSECT.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/DISSECT/lib/DISSECT.jar

Probing: GEO.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/GEO_SPHERE/lib/GEO.addon.jar

Probing: antlr-runtime-4.2.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MASTER/lib/antlr-runtime-4.2.jar

Probing: guava-16.0.1.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MASTER/lib/guava-16.0.1.jar

Probing: jackson-annotations-2.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MASTER/lib/jackson-annotations-2.2.3.jar

Probing: jackson-core-2.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MASTER/lib/jackson-core-2.2.3.jar

Probing: jackson-databind-2.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MASTER/lib/jackson-databind-2.2.3.jar

Probing: MASTER.package.v3.0.0.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MASTER/lib/MASTER.package.v3.0.0.jar

Probing: MODEL_SELECTION.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar

Probing: MM.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/morph-models/lib/MM.addon.jar

Probing: guava-15.0.jar Skip loading file:/Users/matzke/Library/Application Support/BEAST/2.2/MultiTypeTree/lib/guava-15.0.jar: contains classs com.google.common.annotations.Beta that is already loaded

Probing: jblas-1.2.3.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MultiTypeTree/lib/jblas-1.2.3.jar

Probing: MultiTypeTree.v4.0.0.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/MultiTypeTree/lib/MultiTypeTree.v4.0.0.jar

Probing: phylodynamics.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/phylodynamics/lib/phylodynamics.addon.jar

Probing: RBS.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/RBS/lib/RBS.addon.jar

Probing: SA.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/SA/lib/SA.addon.jar

Probing: snap.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/SNAPP/lib/snap.addon.jar

Probing: colt.jar Skip loading file:/Users/matzke/Library/Application Support/BEAST/2.2/SubstBMA/lib/colt.jar: contains classs cern.clhep.PhysicalConstants that is already loaded

Probing: SubstBMA.addon.jar Loaded URL file:/Users/matzke/Library/Application Support/BEAST/2.2/SubstBMA/lib/SubstBMA.addon.jar

Library expoTree not found in Phylodynamics lib directory...

Trying java.library.path (set command line argument or copy to run directory

Checking class: beast.phylodynamics.ExactBDSIS

java.lang.UnsatisfiedLinkError: no expoTree in java.library.path

at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1865)

at java.lang.Runtime.loadLibrary0(Runtime.java:870)

at java.lang.System.loadLibrary(System.java:1119)

at beast.phylodynamics.ExactBDSIS.<clinit>(Unknown Source)

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:260)

at beast.util.AddOnManager.find(Unknown Source)

at beast.app.DocMaker.<init>(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

Checking class: beast.evolution.tree.coalescent.GMRFSkyrideLikelihood

java.lang.NoClassDefFoundError: no/uib/cipr/matrix/Vector

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:260)

at beast.util.AddOnManager.find(Unknown Source)

at beast.app.DocMaker.<init>(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

Caused by: java.lang.ClassNotFoundException: no.uib.cipr.matrix.Vector

at java.net.URLClassLoader$1.run(URLClassLoader.java:372)

at java.net.URLClassLoader$1.run(URLClassLoader.java:361)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:360)

at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)

at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

... 7 more

Checking class: beast.evolution.operators.GMRFSkyrideBlockUpdateOperator

java.lang.NoClassDefFoundError: no/uib/cipr/matrix/Matrix

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:260)

at beast.util.AddOnManager.find(Unknown Source)

at beast.app.DocMaker.<init>(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

Caused by: java.lang.ClassNotFoundException: no.uib.cipr.matrix.Matrix

at java.net.URLClassLoader$1.run(URLClassLoader.java:372)

at java.net.URLClassLoader$1.run(URLClassLoader.java:361)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:360)

at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)

at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

... 7 more

beast.app.beauti.BeautiAlignmentProvider => Class for creating new alignments to be edited by AlignmentListInputEditor

beast.app.beauti.BeautiConfig => Beauti configuration object, used to find Beauti configuration information from Beauti template files.

beast.app.beauti.BeautiConnector => Specifies which part of the template get connected to the main network

beast.app.beauti.BeautiDiscreteTraitProvider => Class for creating new alignments to be edited by AlignmentListInputEditor

beast.app.beauti.BeautiDoc => Beauti document in doc-view pattern, not useful in models

beast.app.beauti.BeautiLocationTraitProvider => Class for creating new alignments to be edited by AlignmentListInputEditor

beast.app.beauti.BeautiMorphModelAlignmentProvider => Class for creating new alignments to be edited by AlignmentListInputEditor Class for creating new partitions for morphological data to be edited by AlignmentListInputEditor

beast.app.beauti.BeautiPanelConfig => Defines properties for custom panels in Beauti

beast.app.beauti.BeautiSLocationTraitProvider => Class for creating new alignments to be edited by AlignmentListInputEditor Location provider for BEAUti template to set up spherical diffusion models

beast.app.beauti.BeautiSubTemplate => Template that specifies which sub-net needs to be created when a plugin of a paricular class is created.

beast.app.draw.BEASTObjectSet => Set of plugins to represent partially finished models in GUIs

beast.app.seqgen.MergeDataWith => Helper for Sequence Simulator, allows specifying template input file and destination output file

beast.app.seqgen.SequenceSimulator => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Performs random sequence generation for a given site model. Sequences for the leave nodes in the tree are returned as an alignment.

beast.app.seqgen.SimulatedAlignment => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data An alignment containing sequences randomly generated using agiven site model down a given tree.

beast.app.shell.Plot => Contains a series to be used in a plot Creates a chart of data and specifies all details of the style of a chart

Chart style (chartType, chartBackgroundColor, chartFontColor, chartPadding),

Chart title (chartTitleFont, isChartTitleVisible, isChartTitleBoxVisible, chartTitleBoxBackgroundColor, chartTitleBoxBorderColor, chartTitlePadding),

Chart legend (isLegendVisible, legendBackgroundColor, legendBorderColor, legendFont, legendPadding, legendSeriesLineLength, legendPosition),

Chart axes (xAxisTitleVisible, yAxisTitleVisible, axisTitleFont, xAxisTicksVisible, yAxisTicksVisible, axisTickLabelsFont, axisTickMarkLength, axisTickPadding, axisTickMarksColor, axisTickMarksStroke, axisTickLabelsColor, isAxisTicksLineVisible, isAxisTicksMarksVisible, plotPadding, axisTitlePadding, xAxisTickMarkSpacingHint, yAxisTickMarkSpacingHint, isXAxisLogarithmic, isYAxisLogarithmic, xAxisMin, xAxisMax, yAxisMin, yAxisMax, axisTickSpaceRatio),

Chart plot area (isPlotGridLinesVisible, plotBackgroundColor, plotBorderColor, isPlotBorderVisible, isPlotTicksMarksVisible, plotGridLinesColor, plotGridLinesStroke),

Bar charts (barWidthPercentage, isBarsOverlapped),

Line, scatter, area charts (markerSize),

Error bars (errorBarsColor), and

Formatting (datePattern, locale, timezone, normalDecimalPattern, scientificDecimalPattern)

beast.app.shell.Series => Contains a series to be used in a plot

beast.continuous.AbstractMultivariateTraitLikelihood not documented :null

beast.continuous.FullyConjugateMultivariateTraitLikelihood not documented :beast.continuous.FullyConjugateMultivariateTraitLikelihood

beast.continuous.IntegratedMultivariateTraitLikelihood not documented :beast.continuous.IntegratedMultivariateTraitLikelihood

beast.continuous.MultivariateDiffusionModel => Substitution model that can deal with an alignment containing continuous data something to do with multi variate diffusion...

beast.continuous.SampledMultivariateTraitLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model AbstractMultivariateTraitLikelihood ported from BEAST1 SampledMultivariateTraitLikelihood ported from BEAST1

beast.core.BEASTObject not documented :null

beast.core.CalculationNode not documented :null

beast.core.DataNode => Represents some piece of data for which a likelihood can be calculated

beast.core.Distribution not documented :null

beast.core.FilteredValuable => Plugin that performs calculations based on the State. selects values from a parameter, for instance all even indexed entries

beast.core.Likelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Takes a collection of distributions, typically a number of likelihoods and priors and combines them into the compound of these distributions typically interpreted as the posterior. Represents one of more likelihoods which represent the probability of some data (e.g. a sequence alignment), possibly conditioned on one or more DataNodes (e.g. a Tree or set of Parameters). The class checks that Data has not defined more than one likelihood.

beast.core.Logger => Logs results of a calculation processes on regular intervals.

beast.core.MCMC => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results.

beast.core.MCMC2 => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results.

beast.core.Operator not documented :null

beast.core.OperatorSchedule => Specify operator selection and optimisation schedule

beast.core.Posterior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Posterior, consisting of a prior and a likehood

beast.core.Runnable not documented :null

beast.core.State => The state represents the current point in the state space, and maintains values of a set of StateNodes, such as parameters and trees. Furthermore, the state manages which parts of the model need to be stored/restored and notified that recalculation is appropriate.

beast.core.StateNode not documented :null

beast.core.parameter.BooleanParameter => Plugin that performs calculations based on the State. A node that can be part of the state. A parameter represents a value in the state space that can be changed by operators. A Boolean-valued parameter represents a value (or array of values if the dimension is larger than one) in the state space that can be changed by operators.

beast.core.parameter.BooleanParameterList => Plugin that performs calculations based on the State. A node that can be part of the state. State node representing a list of parameter objects, used for model selection problems. The parameters involved are not instances of Parameter.Base, but are instead instances of a local class QuietParameter which is not itself a StateNode. All constituent parameters must have identical dimensions and bounds. State node describing a list of boolean parameters.

beast.core.parameter.CompoundValuable => Plugin that performs calculations based on the State. Summarizes a set of valuables so that for example a rate matrix can be specified that uses a parameter in various places in the matrix.

beast.core.parameter.DPPointer => Plugin that performs calculations based on the State. A node that can be part of the state. Array that points to some set of parameters

beast.core.parameter.DPValuable => Plugin that performs calculations based on the State. Summarizes a set of valuables from a Dirichlet prior process

beast.core.parameter.GeneralParameterList not documented :null

beast.core.parameter.IntegerParameter => Plugin that performs calculations based on the State. A node that can be part of the state. A parameter represents a value in the state space that can be changed by operators. An integer-valued parameter represents a value (or array of values if the dimension is larger than one) in the state space that can be changed by operators.

beast.core.parameter.IntegerParameterList => Plugin that performs calculations based on the State. A node that can be part of the state. State node representing a list of parameter objects, used for model selection problems. The parameters involved are not instances of Parameter.Base, but are instead instances of a local class QuietParameter which is not itself a StateNode. All constituent parameters must have identical dimensions and bounds. State node describing a list of integer-valued parameters.

beast.core.parameter.InverseMatrixLogger => Use this class to print the inverse of a square matrix.

beast.core.parameter.Map not documented :null

beast.core.parameter.Parameter$Base not documented :null

beast.core.parameter.ParameterList => Plugin that performs calculations based on the State. A node that can be part of the state. This class stores a list of parameters and the size of the list can change.

beast.core.parameter.ParameterMeanLogger => Use this class to print the mean value of a ParameterList.

beast.core.parameter.PointerMean => Plugin that performs calculations based on the State. This class is used to scale things. This object returns the mean values of a vector parameters to which the DPPointer refers.

beast.core.parameter.QuietRealParameter => Plugin that performs calculations based on the State. A node that can be part of the state. A parameter represents a value in the state space that can be changed by operators. A real-valued parameter represents a value (or array of values if the dimension is larger than one) in the state space that can be changed by operators. A real parameter class that allows values to be set quietly. It's convenience is beyond imagination.

beast.core.parameter.RealParameter => Plugin that performs calculations based on the State. A node that can be part of the state. A parameter represents a value in the state space that can be changed by operators. A real-valued parameter represents a value (or array of values if the dimension is larger than one) in the state space that can be changed by operators.

beast.core.parameter.RealParameterList => Plugin that performs calculations based on the State. A node that can be part of the state. State node representing a list of parameter objects, used for model selection problems. The parameters involved are not instances of Parameter.Base, but are instead instances of a local class QuietParameter which is not itself a StateNode. All constituent parameters must have identical dimensions and bounds. State node describing a list of real-valued parameters.

beast.core.parameter.RealParameterWrapper not documented :beast.core.parameter.RealParameterWrapper

beast.core.util.CompoundDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Takes a collection of distributions, typically a number of likelihoods and priors and combines them into the compound of these distributions typically interpreted as the posterior.

beast.core.util.Count => Plugin that performs calculations based on the State. Reports the number of items in a list.

beast.core.util.ESS => Report effective sample size of a parameter or log values from a distribution. This uses the same criterion as Tracer and assumes 10% burn in.

beast.core.util.Indices => Plugin that performs calculations based on the State. Reports the index of the parameter to which each of the pointer index points.

beast.core.util.LoggableSum => Logs the sum of anything that is Valuable

beast.core.util.ParameterConstrainer => Plugin that performs calculations based on the State. Class to constrain a multi-dimensional parameter to have a certain value (like 0) at a certain time range

beast.core.util.PrintListIDNumber => Plugin that performs calculations based on the State. This class prints the ID number of parameters in a ParameterList

beast.core.util.PrintPointerIDNumber => Plugin that performs calculations based on the State. This class prints the ID number of parameters in a ParameterList This class prints the ID numbers of a list of parameters to which a DPPointer refers.

beast.core.util.Sum => Plugin that performs calculations based on the State. calculates sum of a valuable

beast.evolution.alignment.Alignment => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data

beast.evolution.alignment.AlignmentFromTrait => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data Treats trait on taxa as single site alignment

beast.evolution.alignment.AlignmentFromTraitMap => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data Creates and alignment of continuous data, such as a geographic location, from a trait set

beast.evolution.alignment.AlignmentSubset => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data The class serves as a wrapper and only returns a subset of columns defined by the user.

beast.evolution.alignment.AscertainedAlignment => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data Alignemnt that allows ascertainment correction

beast.evolution.alignment.Cognate => These are the entity that is compared across lineages.

beast.evolution.alignment.CognateAlignment => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data This class implements the alignment for cognate data.

beast.evolution.alignment.FilteredAlignment => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data Alignemnt based on a filter operation on another alignment

beast.evolution.alignment.OldWVAlignment not documented :beast.evolution.alignment.OldWVAlignment

beast.evolution.alignment.PrunedAlignment => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data Sub-alignment generated by pruning some taxa and/or some sites. Can automatically detect taxa with non-informative data (all sites are ambiguous).

beast.evolution.alignment.Sequence => Single sequence in an alignment.

beast.evolution.alignment.Taxon => For identifying a single taxon

beast.evolution.alignment.TaxonSet => For identifying a single taxon Set of taxa, useful for instance for multi-gene analysis

beast.evolution.alignment.distance.Distance$Base => Provides distance between two sequences in an alignment

beast.evolution.alignment.distance.F84Distance => Provides distance between two sequences in an alignment compute HKY corrected distance

beast.evolution.alignment.distance.HammingDistance => Provides distance between two sequences in an alignment Hamming distance is the mean number of characters that differ between sequences. Note that unknowns are not ignored, so if both are unknowns '?' the distance is zero.

beast.evolution.alignment.distance.JukesCantorDistance => Provides distance between two sequences in an alignment compute jukes-cantor corrected distance

beast.evolution.alignment.distance.SMMDistance => Provides distance between two sequences in an alignment Calculate the distance between different microsatellite alleles

beast.evolution.branchratemodel.BranchRateModel$Base not documented :null

beast.evolution.branchratemodel.RandomLocalClockModel => Random Local Clock Model, whatever that is....

beast.evolution.branchratemodel.RateStatistic => A statistic that tracks the mean, variance and coefficent of variation of rates. It has three dimensions, one for each statistic.

beast.evolution.branchratemodel.StrictClockModel => Defines a mean rate for each branch in the beast.tree.

beast.evolution.branchratemodel.SynchronizableUCRelaxedClock => Defines an uncorrelated relaxed molecular clock.

beast.evolution.branchratemodel.UCRelaxedClockModel => Defines an uncorrelated relaxed molecular clock.

beast.evolution.datatype.Aminoacid => DataType for amino acids.

beast.evolution.datatype.Binary => Datatype for binary sequences

beast.evolution.datatype.ContinuousDataType => Datatype for capturing continuous data, such as geographic locations

beast.evolution.datatype.DataType$Base not documented :null

beast.evolution.datatype.IntegerData => Datatype for integer sequences

beast.evolution.datatype.IntegerData2 => Datatype for integer sequences

beast.evolution.datatype.LanguageIntegerData => Data type for languages coded as numbers.

beast.evolution.datatype.LocationDataType => Datatype for capturing continuous data, such as geographic locations Datatype for representing geographic locations in 2 dimension, latitude x longitude

beast.evolution.datatype.Nucleotide => Nucleotide datatype for DNA sequences

beast.evolution.datatype.StandardData => Integer data type to describe discrete morphological characters with polymorphisms

beast.evolution.datatype.TwoStateCovarion => Datatype for two state covarion sequences

beast.evolution.datatype.UserDataType => User defined datatype. Allows custom symbols to map onto statesets.

beast.evolution.likelihood.AncestralStateTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376.

beast.evolution.likelihood.BeagleTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. Uses Beagle library to calculate Tree likelihood

beast.evolution.likelihood.CompoundTempTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Takes a collection of distributions, typically a number of likelihoods and priors and combines them into the compound of these distributions typically interpreted as the posterior. This is a collection of temporary tree likelihoods that attempts to facilitate multithreading computation.

beast.evolution.likelihood.DPMultiAlignmentTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. A class that is able compute the likelihood for multiple alignments when the across-site rates are also partitioned.

beast.evolution.likelihood.DPMultiTreesTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. DPTreeLikelihood that allows to take up multiple alignments/trees.

beast.evolution.likelihood.DPSepMultiTreesTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. Tree likelihood that supports independent Dirichlet process priors on the partitionings of substitution model and rate. Tree likelihood that supports independent Dirichlet process priors on the partitionings of substitution model and rate with multiple alignments/trees.

beast.evolution.likelihood.DPSepTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. Tree likelihood that supports independent Dirichlet process priors on the partitionings of substitution model and rate.

beast.evolution.likelihood.DPTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together.

beast.evolution.likelihood.DummyDPSepTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. Tree likelihood that supports independent Dirichlet process priors on the partitionings of substitution model and rate. This class is for testing purpose.

beast.evolution.likelihood.DummyDPTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. This class is for testing purpose.

beast.evolution.likelihood.DummyTempTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. This class is well useful for testing purpose.

beast.evolution.likelihood.DummyTempWVTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. The tree likelihood used and created on the fly during the MCMC when using the DPM model. Tree likelihood supports alignment pattern weights to change during the MCMC. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. Pattern weights can be modified. This class is well useful for testing purpose.

beast.evolution.likelihood.ExperimentalTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Calculates the likelihood of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376.

beast.evolution.likelihood.GenericTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model

beast.evolution.likelihood.LeafTrait => Plugin that performs calculations based on the State. For associating a taxon with its parameter

beast.evolution.likelihood.MixtureTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. Tree likelihood that can handle a general mixture model efficiently

beast.evolution.likelihood.MultiAlignmentTempTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. Temporary likelihood that can take up multiple alignments.

beast.evolution.likelihood.MultiAlignmentTempWVTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. The tree likelihood used and created on the fly during the MCMC when using the DPM model. Tree likelihood supports alignment pattern weights to change during the MCMC. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. Pattern weights can be modified. Temporary likelihood calculation class that is able to take up multiple alignments.

beast.evolution.likelihood.MultiTreesSepTempTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. The tree likelihood used by the operators when using independent DPPs to the substitution model and rate partitioning.

beast.evolution.likelihood.MultiTreesTempTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. TempTreeLikelihood that can handle multiple alignment/trees.

beast.evolution.likelihood.MultiTreesTempWVTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Weight variable tree likelihood that can handle multiple trees.

beast.evolution.likelihood.NewWVTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. The tree likelihood used and created on the fly during the MCMC when using the DPM model. Tree likelihood supports alignment pattern weights to change during the MCMC.

beast.evolution.likelihood.PartitionPositionLogger => Logs the position of partion boundaries based on partition lengths

beast.evolution.likelihood.PartitionProvider => Plugin that performs calculations based on the State. Provides dynamic partitioning of an alignment, splitting it in several parts with its own substitution models

beast.evolution.likelihood.PartitionProviderByCodon => Plugin that performs calculations based on the State. Provides dynamic partitioning of an alignment, splitting it in several parts with its own substitution models Splits alignment into partititions by lengths, and subdivides these partitions by codon position

beast.evolution.likelihood.PartitionedTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. Calculates the likelihood of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376.

beast.evolution.likelihood.PointerLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. This class is probably used for testing.

beast.evolution.likelihood.QuietTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. The tree likelihood used and created on the fly during the MCMC when using the DPM model.

beast.evolution.likelihood.SepTempTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. The tree likelihood used by the operators when using independent DPPs to the substitution model and rate partitioning.

beast.evolution.likelihood.SepTempWVTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. The tree likelihood used and created on the fly during the MCMC when using the DPM model. Tree likelihood supports alignment pattern weights to change during the MCMC. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. Pattern weights can be modified. The tree likelihood used by the operators when using independent DPPs to the substitution model and rate partitioning. It allows pattern weights to be modified.

beast.evolution.likelihood.SlowDPSepTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. Does a lot of unnecessary calculation (calculates likelihoods at sites that are not required). Used for testing. Does a lot of unnecessary calculation (calculates likelihoods at sites that are not required). Used for testing.

beast.evolution.likelihood.SlowDPTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Tree likelihood that supports Dirichlet process mixture model on the partitionings of substitution model and rate together. Does a lot of unnecessary calculation (calculates likelihoods at sites that are not required). Used for testing.

beast.evolution.likelihood.TempSiteTreeLikelihood not documented :beast.evolution.likelihood.TempSiteTreeLikelihood

beast.evolution.likelihood.TempTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning.

beast.evolution.likelihood.TempWVTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. The tree likelihood used and created on the fly during the MCMC when using the DPM model. Tree likelihood supports alignment pattern weights to change during the MCMC. Used to compute the tree likelihood for operators that samples the partitioning space. Used when there is only one partitioning. Pattern weights can be modified.

beast.evolution.likelihood.ThreadedTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Calculates the likelihood of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376.

beast.evolution.likelihood.TraitedTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. Performs peeling algorithm over a tree using a trait as values for tips instead of a sequence

beast.evolution.likelihood.TreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376.

beast.evolution.likelihood.WVTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. This class is used to tree likelihood with variable pattern weights.

beast.evolution.operators.BitFlipBSSVSOperator => Proposes a move in state space. Flip one bit in an array of boolean bits and scale the BSSVS parameter accordingly. The hastings ratio is designed so that all subsets of vectors with the same number of 'on' bits are equiprobable.

beast.evolution.operators.BitFlipOperator => Proposes a move in state space. Flip one bit in an array of boolean bits. The hastings ratio is designed so that all subsets of vectors with the same number of 'on' bits are equiprobable.

beast.evolution.operators.CategoricalPDirichletPriorSampler => Proposes a move in state space. This is the Gibb sampler for categorial distribution assuming a Dirichlet prior.

beast.evolution.operators.CategoryDeltaExchangeOperator => Proposes a move in state space. This class re-assigns a random number of sites in a randomly picked category to another randomly picked category.

beast.evolution.operators.CombinedOperator => Proposes a move in state space. Combines propoosals by randomly selecting from two groups of operators

beast.evolution.operators.DeltaExchangeOperator => Proposes a move in state space. A generic operator for use with a sum-constrained (possibly weighted) vector parameter.

beast.evolution.operators.DirichletProcessPriorGibbsSampler => Proposes a move in state space. Gibbs sampler with a Dirichlet process prior.

beast.evolution.operators.DirichletProcessPriorSampler => Proposes a move in state space. Performs gibbs sampling when a dirichlet process prior is used.

beast.evolution.operators.Exchange => Proposes a move in state space. This operator changes a beast.tree. Implements branch exchange operations. There is a NARROW and WIDE variety. The narrow exchange is very similar to a rooted-beast.tree nearest-neighbour interchange but with the restriction that node height must remain consistent.

beast.evolution.operators.ExchangeForZeroBranchSampledAncestorTrees => Proposes a move in state space. This operator changes a beast.tree. Implements branch exchange operations. There is a NARROW and WIDE variety. The narrow exchange is very similar to a rooted-beast.tree nearest-neighbour interchange but with the restriction that node height must remain consistent. Implement Narrow and Wide Exchange for sampled ancestor trees.Narrow move chooses a random internal node (not a fake node) with two non-leaf children.Then it takes the older child of this node and exchange one of its children (or just a childif there is only one) with the younger child. Wide remains the same as for regular trees.

beast.evolution.operators.ExtendedRealRandomWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- windowSize. This random walk operator performs random-walk with different window sizes on different indices of a parameter of dimension > 1.

beast.evolution.operators.ExtendedUpDownOperator => Proposes a move in state space. Same as an updown operator but can scale parameters in exponential space.

beast.evolution.operators.FasterRateDPPGibbsSampler => Proposes a move in state space. An attempt to speed up this sampler by using multithreading.

beast.evolution.operators.GeneralIntegerOperator => Proposes a move in state space. Operator to draw integer values from a user specified distribution

beast.evolution.operators.IntRandomWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the integer parameter and perturbs the value a random amount within +/- windowSize.

beast.evolution.operators.IntRandomWalkWithExclusion => Proposes a move in state space.

beast.evolution.operators.IntSwapWithExclusion => Proposes a move in state space. A generic operator swapping a one or more pairs in a multi-dimensional integer parameter

beast.evolution.operators.IntUniformOperator => Proposes a move in state space. A uniform random operator that selects a random dimension of the integer parameter and picks a new random value within the bounds.

beast.evolution.operators.IntUniformWithExclusion => Proposes a move in state space. Assign one or more parameter values (excluding negative values) to a uniformly selected value in its range.

beast.evolution.operators.IntegerRandomWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- integer windowSize.

beast.evolution.operators.JointOperator => Proposes a move in state space. Operator which allows multiple operators to be chained together. This is only correct when each operator acts on a different part of the state.

beast.evolution.operators.JumpToPoint => Proposes a move in state space.

beast.evolution.operators.LeafToSampledAncestorJump => Proposes a move in state space. This operator changes a beast.tree. Implements a narrow move between trees of different dimensions (number of nodes in trees).It takes a random sampled node which is either a leaf with the younger siblingor a sampled internal node. In the first case, the leaf becomes a sampled internal node by replacing its parent (the height of the leaf remains unchanged). In the second case, the sampled internal node becomes a leaf by inserting a new parent node at a height which is uniformly chosen on the interval between the sampled node height and its old parent height.

beast.evolution.operators.MeanMVNSampler => Proposes a move in state space. This is a sampler for the mean vector of a multivariate normal distribution when a Multivariate normal prior is applied.

beast.evolution.operators.MultiPointerSwapOperator => Proposes a move in state space. This operator random selections a x sites from two clusters and switches the assignment.

beast.evolution.operators.MultiScaleOperator => Proposes a move in state space. This element represents an operator that scales multiple parameters in the same direction. Each operation involves selecting a scale uniformly at random between scaleFactor and 1/scaleFactor.

beast.evolution.operators.NetworkIntRandomWalkOperator => Proposes a move in state space. Performs a random walk on a network which a single connected component.

beast.evolution.operators.NodeReheight => Proposes a move in state space. This operator changes a beast.tree. Tree operator which randomly changes the height of a node, then reconstructs the tree from node heights.

beast.evolution.operators.NtdBMADPPGibbsSampler => Proposes a move in state space. Gibbs sampler with DPP for NtdBMA.

beast.evolution.operators.NtdBMAPointersSwapOperator => Proposes a move in state space. This operator swaps sites from different substitution model categories.

beast.evolution.operators.NtdBMARateDPPGibbsSampler => Proposes a move in state space. Gibbs sampler with DPP for NtdBMA and rate having the same partition scheme.

beast.evolution.operators.NtdBMARatePointersSwapOperator => Proposes a move in state space. This operator swaps sites from different substitution model and rate categories.

beast.evolution.operators.NtdBMARateSAMSPriorOperator => Proposes a move in state space. Operator that splits and merges categories of substitution model and rate. The substitution model and rate shares the same partition scheme.

beast.evolution.operators.NtdBMASAMSPriorOperator => Proposes a move in state space. Operator that splits and merges categories of substitution model.

beast.evolution.operators.NtdBMASAMSRandomWalkOperator => Proposes a move in state space. Operator that splits and merges categories of substitution model, test phase 2.

beast.evolution.operators.NtdBMASAMSTempOperator => Proposes a move in state space. Operator that splits and merges categories of substitution model, test phase 1.

Programmer error: input rule should be REQUIRED for this Input constructor (parameter)

beast.evolution.operators.PLDeltaExchangeOperator => Proposes a move in state space. A generic operator for use with sum-constrained (possibly weighted) vector parameters in a list.

beast.evolution.operators.PLExtendedRealRandomWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- windowSize. This random walk operator performs random-walk with different window sizes on different indices of a parameter of dimension > 1. This random walk operator performs is adjusted so that it can perform extended random-walk on a list of parameters.

beast.evolution.operators.PLIntegerRandomWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- integer windowSize. A random walk operator that selects a random dimension of a random RealParameter from ParameterList and perturbs the value a random amount within +/- integer windowSize.

beast.evolution.operators.PLNetworkIntRandomWalkOperator => Proposes a move in state space. Performs a random walk on a network which a single connected component. Performs a random walk on a network which a single connected component for items in a list.

beast.evolution.operators.PLScaleOperator => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified. ScaleOperator performed on a list of parameters.

beast.evolution.operators.PickIndicatorOperator => Proposes a move in state space. Propose a new set of indicators independent of the previous state

beast.evolution.operators.PrecisionMatrixGibbsOperator => Proposes a move in state space.

beast.evolution.operators.PrecisionWishartSampler => Proposes a move in state space. This is a sampler for the precision matrix of a multivariate normal distribution when a Wishart prior is applied.

beast.evolution.operators.RBOperator => Proposes a move in state space. Operator for RB-SubstitutionModel to jump between states in the hierarchy

beast.evolution.operators.RBScaleOperator => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified. Scale operator for the RB-Substitution model, which scales only those ratest that are in use

beast.evolution.operators.RateDPPGibbsSampler => Proposes a move in state space. Gibbs sampler with DPP for site rate.

beast.evolution.operators.RatePointersSwapOperator => Proposes a move in state space. Operator that splits and merges categories of substitution rate.

beast.evolution.operators.RateSAMSPriorOperator => Proposes a move in state space. Operator that splits and merges categories of substitution rate.

beast.evolution.operators.RealRandomWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- windowSize.

beast.evolution.operators.RegressionGibbsEffectOperator => Proposes a move in state space. ...

beast.evolution.operators.RegressionGibbsPrecisionOperator => Proposes a move in state space. ???

beast.evolution.operators.RestrictedSubtreeSlide => Proposes a move in state space. This operator changes a beast.tree. Moves the height of an internal node along the branch. If it moves up, it can exceed the root and become a new root. If it moves down, it may need to make a choice which branch to slide down into. Subtree-slide operator that only considers part of the tree defined by the predecessors of a set of clades.

beast.evolution.operators.RootHeightScaleOperator => Proposes a move in state space. This operator changes a beast.tree. Operator for scaling only the root of a tree

beast.evolution.operators.RootTraitRandowWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- windowSize. Random walk opeartor root of a tree trait

beast.evolution.operators.SAExchange => Proposes a move in state space. This operator changes a beast.tree. Implements branch exchange operations. There is a NARROW and WIDE variety. The narrow exchange is very similar to a rooted-beast.tree nearest-neighbour interchange but with the restriction that node height must remain consistent. Implement Narrow and Wide Exchange for sampled ancestor trees.Narrow move chooses a random internal node (not a fake node) with two non-leaf children.Then it takes the older child of this node and exchange one of its children (or just a childif there is only one) with the younger child. Wide remains the same as for regular trees.

beast.evolution.operators.SAScaleOperator => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified.

beast.evolution.operators.SAUniform => Proposes a move in state space. This operator changes a beast.tree. Randomly selects true internal node (i.e. not the root and not a fake node) and move node height uniformly in interval restricted by the node's parent and children.

beast.evolution.operators.SAWilsonBalding => Proposes a move in state space. This operator changes a beast.tree.

beast.evolution.operators.SampledNodeDateRandomWalker => Proposes a move in state space. This operator changes a beast.tree. Randomly moves tip dates on a tree by randomly selecting one from (a subset of) taxa Randomly select a sampled node and shifts the date of the node within a given window

beast.evolution.operators.SampledNodeDateRandomWalkerForZeroBranchSATrees => Proposes a move in state space. This operator changes a beast.tree. Randomly moves tip dates on a tree by randomly selecting one from (a subset of) taxa Randomly select a sampled node and shifts the date of the node within a given window

beast.evolution.operators.ScaleAndSlide => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified.

beast.evolution.operators.ScaleOffsetOperator => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified. Scale a parameter that must always be larger than the height of the tree

beast.evolution.operators.ScaleOperator => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified.

beast.evolution.operators.ScaleOperatorForZeroBranchSATrees => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified.

beast.evolution.operators.SliceOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- windowSize.

beast.evolution.operators.SpecificRealRandomWalkOperator => Proposes a move in state space. A random walk operator that selects a random dimension of the real parameter and perturbs the value a random amount within +/- windowSize. Only apply random walk on the value of a specific index.

beast.evolution.operators.SphereRandomWalker => Proposes a move in state space. Produces proposals of a random walk on a sphere

beast.evolution.operators.SubtreeSlide => Proposes a move in state space. This operator changes a beast.tree. Moves the height of an internal node along the branch. If it moves up, it can exceed the root and become a new root. If it moves down, it may need to make a choice which branch to slide down into.

beast.evolution.operators.SwapOperator => Proposes a move in state space. A generic operator swapping a one or more pairs in a multi-dimensional parameter

beast.evolution.operators.TipDatesRandomWalker => Proposes a move in state space. This operator changes a beast.tree. Randomly moves tip dates on a tree by randomly selecting one from (a subset of) taxa

beast.evolution.operators.TipDatesScaler => Proposes a move in state space. This operator changes a beast.tree. Scales tip dates on a tree by randomly selecting one from (a subset of) taxa

beast.evolution.operators.TraitGibbsOperator => Proposes a move in state space.

beast.evolution.operators.TreeDimensionJump => Proposes a move in state space. This operator changes a beast.tree. Implements a narrow move between trees of different dimensions (number of nodes in trees).It takes a random sampled node which is either a leaf with the younger siblingor a sampled internal node. In the first case, the leaf becomes a sampled internal node by replacing its parent (the height of the leaf remains unchanged). In the second case, the sampled internal node becomes a leaf by inserting a new parent node at a height which is uniformly chosen on the interval between the sampled node height and its old parent height.

beast.evolution.operators.TreeOperator not documented :null

beast.evolution.operators.TreeWithMetaDataRandomWalker => Proposes a move in state space. Operator that uses a standard TreeOperator to change the topology of the tree, then changes metadata (such as rate categories for relaxed clock) associated with only those nodes in the tree that are changed due to the TreeOperator.

beast.evolution.operators.Uniform => Proposes a move in state space. This operator changes a beast.tree. Randomly selects true internal tree node (i.e. not the root) and move node height uniformly in interval restricted by the nodes parent and children.

beast.evolution.operators.UniformForZeroBranchSATrees => Proposes a move in state space. This operator changes a beast.tree. Randomly selects true internal node (i.e. not the root and not a fake node) and move node height uniformly in interval restricted by the node's parent and children.

beast.evolution.operators.UniformOperator => Proposes a move in state space. Assign one or more parameter values to a uniformly selected value in its range.

beast.evolution.operators.UpDownOperator => Proposes a move in state space. This element represents an operator that scales two parameters in different directions. Each operation involves selecting a scale uniformly at random between scaleFactor and 1/scaleFactor. The up parameter is multiplied by this scale and the down parameter is divided by this scale.

beast.evolution.operators.WilsonBalding => Proposes a move in state space. This operator changes a beast.tree. Implements the unweighted Wilson-Balding branch swapping move. This move is similar to one proposed by WILSON and BALDING 1998 and involves removing a subtree and re-attaching it on a new parent branch. See <a href='http://www.genetics.org/cgi/content/full/161/3/1307/F1'>picture</a>.

beast.evolution.operators.WilsonBaldingForZeroBranchSampledAncestorTrees => Proposes a move in state space. This operator changes a beast.tree.

beast.evolution.operators.WilsonBaldingWithRateCategories => Proposes a move in state space. This operator changes a beast.tree. Implement Wilson Balding operator for (zero branch) sampled ancestor trees and per branch rate categoriesThis version of Wilson Balding operator does not change the root.

beast.evolution.operators.util.Vertex => This class represents a vertex in a network.

beast.evolution.sitemodel.DPMultiAlignRateSiteModel => Plugin that performs calculations based on the State. Parent class of all DP site models. Site model that can handle multiple alignments as well as DPM. Site model that can handle multiple alignments as well as DPM on rates.

beast.evolution.sitemodel.DPMultiAlignSiteModel not documented :null

beast.evolution.sitemodel.DPNtdRateSepSiteModel => Plugin that performs calculations based on the State. Parent class of all DP site models. Parent class of all DP site models that can only handle a single alignment. Manages a list of simple gamma site models. Can create and remove site models on the fly. Used when independent DPPs are applied to the partitioning schemes of the substitution model and rate.

beast.evolution.sitemodel.DPNtdRateSiteModel => Plugin that performs calculations based on the State. Parent class of all DP site models. Parent class of all DP site models that can only handle a single alignment. This class facilitates partition selection by DPP on site rates. Manages a list of simple gamma site models. Can create and remove site models on the fly. Used when a DPP is applied to the partitioning scheme of the substitution model and rate together.

beast.evolution.sitemodel.DPNtdSiteModel => Plugin that performs calculations based on the State. Parent class of all DP site models. Parent class of all DP site models that can only handle a single alignment. This site model class facilitates partition selection by DPP on nucleotide substitution models.

beast.evolution.sitemodel.DPRateSiteModel => Plugin that performs calculations based on the State. Parent class of all DP site models. Parent class of all DP site models that can only handle a single alignment. This class facilitates partition selection by DPP on site rates.

beast.evolution.sitemodel.DPSingleAlignSiteModel not documented :null

beast.evolution.sitemodel.DPSiteModel not documented :null

beast.evolution.sitemodel.DefaultMixtureSiteModel => Defines mutation rate and gamma distributed rates across sites (optional) and proportion of the sites invariant (also optional). Gamma site model -- for testing Mixture treelikelihood

beast.evolution.sitemodel.DummySiteModel => Defines mutation rate and gamma distributed rates across sites (optional) and proportion of the sites invariant (also optional). This site model is used for computing tree likelihoods for operator move. It is used by DP samplers so that we can use the same site model object over and over again which is required by the move.

beast.evolution.sitemodel.EfficientDPNtdRateSepSiteModel => Plugin that performs calculations based on the State. Parent class of all DP site models. Parent class of all DP site models that can only handle a single alignment. Manages a list of simple gamma site models. Can create and remove site models on the fly. Used when independent DPPs are applied to the partitioning schemes of the substitution model and rate. An incomplete attempt to improve the efficiency of computation.

beast.evolution.sitemodel.GeneralJC69 => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. A more general version of JC69.

beast.evolution.sitemodel.MixtureSiteModel => Defines mutation rate and gamma distributed rates across sites (optional) and proportion of the sites invariant (also optional). Gamma site model -- for testing Mixture treelikelihood General Mixture Model from Stephane Guindon

beast.evolution.sitemodel.MixtureSubstModel => Plugin that performs calculations based on the State. One component of a Mixture Site Model

beast.evolution.sitemodel.QuietSiteModel not documented :beast.evolution.sitemodel.QuietSiteModel

beast.evolution.sitemodel.SiteModel => Defines mutation rate and gamma distributed rates across sites (optional) and proportion of the sites invariant (also optional).

beast.evolution.sitemodel.SiteModelInterface$Base not documented :null

beast.evolution.speciation.BirthDeathGernhard08Model => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Pure birth model (i.e. no deaths) Birth Death model based on Gernhard 2008. This derivation conditions directly on fixed N taxa. The inference is directly on b-d (strictly positive) and d/b (constrained in [0,1)) Verified using simulated trees generated by Klass tree sample. (http://www.klaashartmann.com/treesample/) Sampling proportion not verified via simulation. Proportion set by default to 1, an assignment which makes the expressions identical to the expressions before the change.

beast.evolution.speciation.BirthDeathSkylineModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Adaptation of Tanja Stadler's BirthDeathSamplingModel, to allow for birth and death rates to change at times t_i

Programmer error: input rule should be REQUIRED for this Input constructor (relativeDeathRate)

Programmer error: input rule should be REQUIRED for this Input constructor (sampleProbability)

beast.evolution.speciation.CalibratedBirthDeathModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Birth-Death prior with calibrated monophyletic clades. With this prior, the marginal distribution of the calibrated nodes (the root age of the clade) is identical to the specified calibration, and the density ratio between trees with equal calibration values is equal to the ratio under the Birth-Death prior.

beast.evolution.speciation.CalibratedYuleInitialTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. A tree compatible with a set of monophyletic clades and hard limits on the clade root.

beast.evolution.speciation.CalibratedYuleModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Yule prior with calibrated monophyletic clades. With this prior, the marginal distribution of the calibrated nodes (the MRCA of clades) is identical to the specified calibration, but the Yule is not preserved over the whole tree space, only among sub-spaces.

beast.evolution.speciation.CalibrationPoint => Specification of a single calibration point of the calibrated Yule.

beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule Calculates probability of gene tree conditioned on a species tree (multi-species coalescent)

beast.evolution.speciation.RandomGeneTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. This class provides the basic engine for coalescent simulation of a given demographic model over a given time period. Generates a random gene tree conditioned on a species tree, such that the root of the species tree is lower than any coalescent events in the gene tree

beast.evolution.speciation.RandomLocalYuleModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Experimental code with unknown use. If you know, fill this in. A speciation model of a Yule process whose rate of birth changes at different points in the tree.

beast.evolution.speciation.SABDSamplingThroughTimeModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Calculate tree density under Birth Death Sampling Through Time Model for Epidemics that is the BDM where an individual is sampled at a time with a constant rate psi and where an individual becomes noninfectious immediately after the samplingwith a constant probability r

beast.evolution.speciation.SABirthDeathModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Calculate tree density under Birth Death Sampling Through Time Model for Epidemics that is the BDM where an individual is sampled at a time with a constant rate psi and where an individual becomes noninfectious immediately after the samplingwith a constant probability r

beast.evolution.speciation.SpeciesTreeDistribution not documented :null

beast.evolution.speciation.SpeciesTreeLogger => Logs tree annotated with metadata in StarBeast format

beast.evolution.speciation.SpeciesTreePrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule Species tree prior for *BEAST analysis

beast.evolution.speciation.StarBeastStartState => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. Set a starting point for a *BEAST analysis from gene alignment data.

beast.evolution.speciation.TreeTopFinder => Plugin that performs calculations based on the State. Finds height of highest tree among a set of trees

beast.evolution.speciation.UltrametricSpeciationModel not documented :null

beast.evolution.speciation.YuleModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Pure birth model (i.e. no deaths)

beast.evolution.speciation.YuleModelWithScaling => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Pure birth model (i.e. no deaths) This yule model takes an extra parameter so that node heights are scaled correctly. This is used when we cannot estimate time and substitution rate(s) separately.

beast.evolution.substitutionmodel.BinaryCovarion => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. Covarion model for Binary data

beast.evolution.substitutionmodel.Blosum62 => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG. BLOSUM62 model of amino acid evolution Henikoff, S., and J. G. Henikoff. 1992. PNAS USA 89:10915-10919.

beast.evolution.substitutionmodel.CPREV => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG. CPREV 45 model of amino acid evolution Adachi, J., P.J. Waddell, W. Martin, and M. Hasegawa. 2000. JME 50:348-358

beast.evolution.substitutionmodel.CladeSubstitutionModel => Substitution model dependent on clades. For each clade a substitution model is specified. For nodes that do not fit in a clade a default substitution model is used.

beast.evolution.substitutionmodel.ContinuousSubstitutionModel not documented :null

beast.evolution.substitutionmodel.DPNtdBMA => Plugin that performs calculations based on the State. A list of SwitchingNtdBMA classes for DPP.

beast.evolution.substitutionmodel.Dayhoff => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG. Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978) A model of evolutionary change in proteins. Dayhoff, M.O. (ed.) Atlas of Protein Sequence Structur., Vol5, Suppl. 3, National Biomedical Research Foundation, Washington DC, pp. 345-352.

beast.evolution.substitutionmodel.EmpiricalSubstitutionModel not documented :null

beast.evolution.substitutionmodel.EpochSubstitutionModel => A substitution model that can change at various threshold dates.

beast.evolution.substitutionmodel.Frequencies => Plugin that performs calculations based on the State. Represents character frequencies typically used as distribution of the root of the tree. Calculates empirical frequencies of characters in sequence data, or simply assumes a uniform distribution if the estimate flag is set to false.

beast.evolution.substitutionmodel.GTR => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. General Time Reversible model of nucleotide evolution. Rates that are not specified are assumed to be 1.

beast.evolution.substitutionmodel.GeneralLazySubstitutionModel => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. Uses a super-relaxed clock model. Note, this should only be used with strict clock models.

beast.evolution.substitutionmodel.GeneralSubstitutionModel => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states.

beast.evolution.substitutionmodel.HKY => HKY85 (Hasegawa, Kishino & Yano, 1985) substitution model of nucleotide evolution.

beast.evolution.substitutionmodel.JTT => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG. * JTT model for amino acid evolution D.T. Jones, W.R. Taylor, and J.M. Thornton The rapid generation of mutation data matrices from protein sequences CABIOS vol. 8 no. 3 1992 pp. 275-282.

beast.evolution.substitutionmodel.JukesCantor => Jukes Cantor substitution model: all rates equal and uniformly distributed frequencies

beast.evolution.substitutionmodel.LazyHKY => HKY85 (Hasegawa, Kishino & Yano, 1985) substitution model of nucleotide evolution. Lazy version of HKY85 substitution model of nucleotide evolution.

beast.evolution.substitutionmodel.LewisMK => LewisMK subtitution model: equal rates, equal frequencies

beast.evolution.substitutionmodel.MTREV => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG. MTREV24 model of amino acid evolution (complete sequence data of mtDNA from 24 vertebrate species) Adachi, J., and Hasegawa, M. 1996. J. Mol. Evol. 42:459-468.

beast.evolution.substitutionmodel.MutationDeathModel => Mutation Death substitution model, can be used as Stochastic Dollo model.

beast.evolution.substitutionmodel.NtdBMA => This class augments the parameter space of GTR to allow selection of nucleotide substitution models.

beast.evolution.substitutionmodel.RB => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. Substitution model for nucleotides that changes where the count input determines the number of parameters used in a hierarchy of models

beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states.

beast.evolution.substitutionmodel.SubstitutionModel$Base not documented :null

beast.evolution.substitutionmodel.SubstitutionModel$NucleotideBase not documented :null

beast.evolution.substitutionmodel.SwitchingNtdBMA => This class augments the parameter space of GTR to allow selection of nucleotide substitution models. This class switches between analytic and numerical computation depends on the substitution model selected.

beast.evolution.substitutionmodel.TN93 => TN93 (Tamura and Nei, 1993) substitution model of nucleotide evolution.

beast.evolution.substitutionmodel.VS => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. Substitution model for nucleotides that changes where the count input determines the number of parameters used in a hierarchy of models

beast.evolution.substitutionmodel.WAG => Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states. A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG. WAG model of amino acid evolution by S. Whelan and N. Goldman. 2000. Bioinformatics ?.

beast.evolution.taxonomy.Taxon not documented :beast.evolution.taxonomy.Taxon

beast.evolution.tree.CladeConstraint => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain.

beast.evolution.tree.ConstrainedRandomTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. This class provides the basic engine for coalescent simulation of a given demographic model over a given time period. Random tree with constraints specified by one tree, just like multiple monophyly.

beast.evolution.tree.FlatMultiTypeTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. A standard BEAST tree representation of a TreeColour object.

beast.evolution.tree.InitParamFromTree => Sets values of a parameter from metadata values associated with a newick tree

beast.evolution.tree.MigrationModel => Plugin that performs calculations based on the State. Basic plugin describing a simple Markovian migration model.

beast.evolution.tree.MonophyleticConstraint => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Enforces groups of taxa to be monophyletic -- have a common mrca that no other taxa have. This can be used as part of the prior. Multiple monophyletic constraints can be handled by adding one set per constraing.

beast.evolution.tree.MultiTypeNode => Nodes in building beast.tree data structure. A node in a multi-type phylogenetic tree.

beast.evolution.tree.MultiTypeTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. A multi-type phylogenetic tree.

beast.evolution.tree.MultiTypeTreeFromNewick => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. A multi-type phylogenetic tree. Class to initialize a MultiTypeTree from single child newick tree with type metadata

beast.evolution.tree.Node => Nodes in building beast.tree data structure.

beast.evolution.tree.PrunedTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. The binary tree generated by pruning a fixed subset of taxa from a source binary tree.

beast.evolution.tree.RandomMultiTypeTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. A multi-type phylogenetic tree. Class to initialize a MultiTypeTree from random tree by adding minimum number of changes needed

beast.evolution.tree.RandomTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. This class provides the basic engine for coalescent simulation of a given demographic model over a given time period.

beast.evolution.tree.RootTrait => Plugin that performs calculations based on the State. A logger for the type of the tree root

beast.evolution.tree.SALogger => Plugin that performs calculations based on the State.

beast.evolution.tree.SATreeLogger => Logs results of a calculation processes on regular intervals.

beast.evolution.tree.SampledAncestorLogger => Plugin that performs calculations based on the State.

beast.evolution.tree.SamplingDate =>

beast.evolution.tree.ScaledTreeHeightLogger => Plugin that performs calculations based on the State. Logger to report height of a tree Scales the tree with the provided scaler and then log it.

beast.evolution.tree.ScaledTreeWithMetaDataLogger => Logs tree annotated with metadata and/or rates Scales the tree with the provided scaler and then log it with metadata.

beast.evolution.tree.Scaler not documented :null

beast.evolution.tree.StructuredCoalescentMultiTypeTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. A multi-type phylogenetic tree. A multi-type tree generated randomly from leaf types anda migration matrix with fixed population sizes.

beast.evolution.tree.TraitSet => A trait set represent a collection of properties of taxons, for the use of initializing a tree. The traits are represented as text content in taxon=value form, for example, for a date trait, wecould have a content of chimp=1950,human=1991,neander=-10000. All white space is ignored, so they canbe put on multiple tabbed lines in the XML. The type of node in the tree determines what happes with this information. The default Node only recognizes 'date', 'date-forward' and 'date-backward' as a trait, but by creating custom Node classes other traits can be supported as well.

beast.evolution.tree.Tree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data.

beast.evolution.tree.TreeDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule

beast.evolution.tree.TreeHeightLogger => Plugin that performs calculations based on the State. Logger to report height of a tree

beast.evolution.tree.TreeHeightValuable => Plugin that performs calculations based on the State. Extract the tree height and return it as a valuable.

beast.evolution.tree.TreeLengthLogger => Plugin that performs calculations based on the State. Reports the length of the tree.

beast.evolution.tree.TreeReport => Logs results of a calculation processes on regular intervals. Modified logger which analyses a list of tree states generatedby an MCMC run.

beast.evolution.tree.TreeScaler => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. This class is used to scale the tree to a certain height.

beast.evolution.tree.TreeTraitMap => Plugin that performs calculations based on the State. Maps nodes in a tree to entries of a parameter

beast.evolution.tree.TreeTraitProvider$Helper =>

beast.evolution.tree.TreeWithMetaDataLogger => Logs tree annotated with metadata and/or rates

beast.evolution.tree.TreeWithTraitLogger => Logs tree annotated with metadata and/or rates

beast.evolution.tree.ZeroBranchSANode => Nodes in building beast.tree data structure.

beast.evolution.tree.ZeroBranchSARandomTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. This class provides the basic engine for coalescent simulation of a given demographic model over a given time period.

beast.evolution.tree.ZeroBranchSATree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data.

beast.evolution.tree.coalescent.BayesianSkyline => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for the generalized skyline plot coalescent.

beast.evolution.tree.coalescent.CauchyPlusConstant => Plugin that performs calculations based on the State. An implementation of a population size function plugin.Also note that if you are dealing with a diploid population N0 will be the number of alleles, not the number of individuals. Population model of the form A/(B*(t-t0)^2 + 1) + C.

beast.evolution.tree.coalescent.Coalescent => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule Calculates the probability of a beast.tree conditional on a population size function. Note that this does not take the number of possible tree interval/tree topology combinations in account, in other words, the constant required for making this a proper distribution that integrates to unity is not calculated (partly, because we don't know how for sequentially sampled data).

beast.evolution.tree.coalescent.CompoundPopulationFunction => Plugin that performs calculations based on the State. An implementation of a population size function plugin.Also note that if you are dealing with a diploid population N0 will be the number of alleles, not the number of individuals. An effective population size function based on coalecent times from a set of trees.

beast.evolution.tree.coalescent.ConstantPopulation => Plugin that performs calculations based on the State. An implementation of a population size function plugin.Also note that if you are dealing with a diploid population N0 will be the number of alleles, not the number of individuals. coalescent intervals for a constant population

beast.evolution.tree.coalescent.ExponentialGrowth => Plugin that performs calculations based on the State. An implementation of a population size function plugin.Also note that if you are dealing with a diploid population N0 will be the number of alleles, not the number of individuals. Coalescent intervals for a exponentially growing population.

beast.evolution.tree.coalescent.ExponentialGrowthPlusConstant => Plugin that performs calculations based on the State. An implementation of a population size function plugin.Also note that if you are dealing with a diploid population N0 will be the number of alleles, not the number of individuals. Population model of the form A*exp(-B*t) + C

beast.evolution.tree.coalescent.PopulationFunction$Abstract not documented :null

beast.evolution.tree.coalescent.SampleOffValues => Proposes a move in state space. Sample values from a distribution

beast.evolution.tree.coalescent.ScaledPopulationFunction => Plugin that performs calculations based on the State. An implementation of a population size function plugin.Also note that if you are dealing with a diploid population N0 will be the number of alleles, not the number of individuals. Scale a demographic function by a constant factor

beast.evolution.tree.coalescent.ScaledTreeIntervals => Plugin that performs calculations based on the State. Extracts the intervals from a tree. Points in the intervals are defined by the heights of nodes in the tree. Use this class the scale the tree intervals to the correct units for coalescent likelihood.

beast.evolution.tree.coalescent.StochasticCoalescentSkyline => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule Coalescent skyline plot coupled with forward simulated SIR epidemiological model (aka the coalescent BDSIR)

beast.evolution.tree.coalescent.StructuredCoalescentTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. A tree generated randomly from the structured coalescent process, with the given population sizes, migration rates and per-deme sample sizes.

beast.evolution.tree.coalescent.TreeIntervals => Plugin that performs calculations based on the State. Extracts the intervals from a tree. Points in the intervals are defined by the heights of nodes in the tree.

beast.geo.GeoSpatialDistribution => Plugin that performs calculations based on the State. Distribution over a geographical area

beast.graphics.AbstractTreeDrawing not documented :null

beast.graphics.ColorPlugin =>

beast.graphics.ColorTable =>

beast.graphics.NodeDecorator =>

beast.graphics.NodeDecorator$1 not documented :Class beast.app.DocMaker can not access a member of class beast.graphics.NodeDecorator$1 with modifiers ""

beast.graphics.NodeTimesDecorator =>

beast.graphics.RootedTreeDrawing => Encapsulates a rooted tree and options to draw it within the context of a TreeDrawingGrid.

beast.graphics.TreeDrawingGrid => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Generates the tree figure in grid format, from input trees into Tikz/PGF format for addition to LaTeX document.

beast.graphics.UnrootedTreeDrawing =>

beast.inference.MCMCParticle => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. MCMC chain that synchronises through files. Can be used with ParticleFilter instead of plain MCMC.

beast.inference.MCMCParticleAsync => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. MCMC chain that synchronises through files. Can be used with ParticleFilter instead of plain MCMC. MCMC chain to be launched by ParticleFilter. It updates its state without synchronisation with any of the other particles.

beast.inference.ML => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. Maximum likelihood throught simple random hill climbing

beast.inference.MultiMCMC => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. Runs multiple MCMC chains in parallel and reports Rubin-Gelman statistic while running the chain for each item in the first log file as well as the maximum difference in clade probability for every pair of chains. Note that log file names should have $(seed) in their name so that the first chain uses the actual seed in the file name and all subsequent chains add one to it.Furthermore, the log and tree log should have the same sample frequency.

beast.inference.PairedPathSampleAnalyser => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Reads logs produces through PairedPathSampler and estimates Bayes factor of the pair of models

Programmer error: input rule should be REQUIRED for this Input constructor (model2)

beast.inference.PairedPathSampler => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Calculate marginal likelihood through path/stepping stone sampling. Perform multiple steps and calculate estimate.Uses multiple threads if specified as command line option to BEAST. Calculate marginal likelihood through path/stepping stone sampling for comparing two models. Perform multiple steps and calculate estimate.Uses multiple threads if specified as command line option to BEAST. This uses the operator schedule of the first model.

beast.inference.PairedPathSamplingStep => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. Calculate marginal likelihood through path sampling for a single step Calculate marginal likelihood through path sampling for a single step when comparing two models

beast.inference.ParticleFilter => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC Inference by particle filter approach. This works only when run with many threads, one per particle is optimal.

beast.inference.PathSampleAnalyser => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Reads logs produces through PathSampler and estimates marginal likelihood

beast.inference.PathSampler => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Calculate marginal likelihood through path/stepping stone sampling. Perform multiple steps and calculate estimate.Uses multiple threads if specified as command line option to BEAST.

beast.inference.PathSamplerFromFile => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Calculate marginal likelihood through path/stepping stone sampling. Perform multiple steps and calculate estimate.Uses multiple threads if specified as command line option to BEAST. Path sampler that takes a BEAST MCMC specification from an external file

beast.inference.PathSamplingStep => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. Calculate marginal likelihood through path sampling for a single step

beast.inference.SimulatedAnnealing => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. Maximum likelihood by simulated annealing

beast.inference.distribution.GeneralizedLinearModel => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. ...

beast.inference.distribution.LinearRegression => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. ... (Log-) linear regression model

beast.inference.distribution.LogisticRegression => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. ... ...

beast.math.distributions.Beta => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Beta distribution, used as prior. p(x;alpha,beta) =

rac{x^{alpha-1}(1-x)^{beta-1}} {B(alpha,beta)} where B() is the beta function. If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.CategoricalDistribution => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. This class represents a discrete distirbution on integers.

beast.math.distributions.ChiSquare => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Chi square distribution, f(x; k) = \frac{1}{2^{k/2}Gamma(k/2)} x^{k/2-1} e^{-x/2} If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.CompoundDirichletProcess => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. The base measure of this Dirichlet process is the product of a list of distributions/densities.

beast.math.distributions.CompoundFossilPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Takes a collection of fossil priors and combines them into the compound of these distributions.

beast.math.distributions.ContinuousCategoricalDistribution => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. For testing only. Don't laugh.

beast.math.distributions.ContinuousCategoricalDistribution2 => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. For testing only. Still don't laugh.

beast.math.distributions.DegenerateBeta => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities.

beast.math.distributions.DegenerateUniform => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities.

beast.math.distributions.Dirichlet => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Dirichlet distribution. p(x_1,...,x_n;alpha_1,...,alpha_n) = 1/B(alpha) prod_{i=1}^K x_i^{alpha_i - 1} where B() is the beta function B(alpha) = prod_{i=1}^K Gamma(alpha_i)/ Gamma(sum_{i=1}^K alpha_i}.

beast.math.distributions.DirichletDistribution => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Dirichlet distribution. p(x_1,...,x_n;alpha_1,...,alpha_n) = 1/B(alpha) prod_{i=1}^K x_i^{alpha_i - 1} where B() is the beta function B(alpha) = prod_{i=1}^K Gamma(alpha_i)/ Gamma(sum_{i=1}^K alpha_i}. Extends Dirichlet class to add the sample method.

beast.math.distributions.DirichletProcess => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. This class that the dirichlet process.

beast.math.distributions.DummyLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. A class that is well uselful for testing things.

beast.math.distributions.ExcludablePrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Produces prior (log) probability of value x.If x is multidimensional, the components of x are assumed to be independent, so the sum of log probabilities of all elements of x is returned as the prior. Just as with Prior, produces log probability of the parameter x. This variant however allows one to explicitly exclude individual elements of multidimensional parameters from the result.

beast.math.distributions.Exponential => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Exponential distribution. f(x;\lambda) = 1/\lambda e^{-x/\lambda}, if x >= 0 If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.FossilCalibration => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Distribution based on fossil information

beast.math.distributions.FossilPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Prior over set of taxa, useful for defining monophyletic constraints and distributions over MRCA times or (sets of) tips of trees Prior based on information from the fossil record

beast.math.distributions.Gamma => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Gamma distribution. for x>0 g(x;alpha,beta) = \frac{beta^{alpha}}{Gamma(alpha)} x^{alpha-1} e^{-beta {x}}If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.IntegerUniformDistribution => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Uniform distribution for integers.

beast.math.distributions.InverseGamma => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Inverse Gamma distribution, used as prior. for x>0 f(x; alpha, beta) =

rac{beta^alpha}{Gamma(alpha)} (1/x)^{alpha + 1}exp(-beta/x) If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.LaplaceDistribution => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Laplace distribution. f(x|\mu,b) = \frac{1}{2b} \exp \left( -\frac{|x-\mu|}{b} \right)The probability density function of the Laplace distribution is also reminiscent of the normal distribution; however, whereas the normal distribution is expressed in terms of the squared difference from the mean ?, the Laplace density is expressed in terms of the absolute difference from the mean. Consequently the Laplace distribution has fatter tails than the normal distribution.

beast.math.distributions.LogNormal => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. A log-normal distribution with mean and variance parameters. Lognormal distribution which takes the parameter precision instead of standard deviation in log space.

beast.math.distributions.LogNormalDistributionModel => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. A log-normal distribution with mean and variance parameters.

beast.math.distributions.MRCAPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Prior over set of taxa, useful for defining monophyletic constraints and distributions over MRCA times or (sets of) tips of trees

beast.math.distributions.MarkovChainDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. A class that produces a distribution chaining values in a parameter through the Gamma distribution. The value of a parameter is assumed to be Gamma distributed with mean as the previous value in the parameter. If useLogNormal is set, a log normal distribution is used instead of a Gamma. If a Jeffrey's prior is used, the first value is assumed to be distributed as 1/x, otherwise it is assumed to be uniform. Handy for population parameters.

beast.math.distributions.MultiMonophyleticConstraint => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Prior over set of taxa, useful for defining multiple monophyletic constraints using a newick format

beast.math.distributions.Multinomial => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. This class implements the multinomial distribution.

beast.math.distributions.MultivariateNormal => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. This class implements the multivariate nromal distribution.

beast.math.distributions.MultivariateNormalDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. MultivariateNormalDistribution ported from BEAST1

beast.math.distributions.Normal => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Normal distribution. f(x) = frac{1}{\sqrt{2\pi\sigma^2}} e^{ -\frac{(x-\mu)^2}{2\sigma^2} } If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.NtdDP => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. This class that the dirichlet process. Dirichlet process for model parameters of nucletoide subsitution model.

beast.math.distributions.OneOnX => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. OneOnX distribution. f(x) = C/x for some normalizing constant C. If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.ParameterListPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Produces prior (log) probability of value x.If x is multidimensional, the components of x are assumed to be independent, so the sum of log probabilities of all elements of x is returned as the prior. This class is a wrapper that provides prior to parameter list.

beast.math.distributions.ParameterListsPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Produces prior (log) probability of value x.If x is multidimensional, the components of x are assumed to be independent, so the sum of log probabilities of all elements of x is returned as the prior. This class is a wrapper that provides prior to parameter list.

beast.math.distributions.ParametricDistribution not documented :null

beast.math.distributions.Poisson => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Poisson distribution, used as prior f(k; lambda)=\frac{lambda^k e^{-lambda}}{k!} If the input x is a multidimensional parameter, each of the dimensions is considered as a separate independent component.

beast.math.distributions.Prior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Produces prior (log) probability of value x.If x is multidimensional, the components of x are assumed to be independent, so the sum of log probabilities of all elements of x is returned as the prior.

beast.math.distributions.RBPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Produces prior (log) probability of value x.If x is multidimensional, the components of x are assumed to be independent, so the sum of log probabilities of all elements of x is returned as the prior. Prior for Reversible-jump Based (RB) substitution model, applies prior only to the rates that are in use

beast.math.distributions.SpecialMRCAPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Prior over set of taxa, useful for defining monophyletic constraints and distributions over MRCA times or (sets of) tips of trees

beast.math.distributions.Uniform => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Uniform distribution over a given interval (including lower and upper values)

beast.math.distributions.UniformDistribution => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Uniform distribution. The one in BEAST 2 is not completed.

beast.math.distributions.Wishart => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. This class implements the Wishart distribution.

beast.math.distributions.WishartDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. WishartDistribution ported from BEAST1

beast.math.statistic.RPNcalculator => Plugin that performs calculations based on the State. RPN calculator to evaluate simple expressions of parameters (Reverse Polish notation is a mathematical notation wherein every operator follows its operands)

beast.phylodynamics.BDSIR => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule A likelihood function for speciation processes. Adaptation of Tanja Stadler's BirthDeathSamplingModel, to allow for birth and death rates to change at times t_i Phylodynamic tree prior that couples compartmental models (e.g. SIR, SIRS) with a piecewise constant birth-death-sampling process.

beast.phylodynamics.epidemiology.CoalescentSIR not documented :null

beast.phylodynamics.epidemiology.CoalescentSimulator => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Performs random tree generation for a given site model.

beast.phylodynamics.epidemiology.CoalescentSimulatorBasic => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. Simulate coalescent trees given a population function.

beast.phylodynamics.epidemiology.CompoundSIROperator => Proposes a move in state space. Operator that simulates new S(E)IR trajectory

beast.phylodynamics.epidemiology.DeterministicCoalescentSIR => Plugin that performs calculations based on the State. Keeps track of deterministic trajectories for effective, infected, and susceptible populations,used by Volz2009TreeDistribution and SIRPopulationFunction

beast.phylodynamics.epidemiology.HybridSEIREpidemic => Plugin that performs calculations based on the State. Simulates a stochastic forward SIR, SEIR or SIRS epidemic

beast.phylodynamics.epidemiology.HybridTrajectorySingleLocationSimulator => Proposes a move in state space. Operator that simulates new S(E)IR trajectory

beast.phylodynamics.epidemiology.SIRPopulationFunction => Plugin that performs calculations based on the State. An implementation of a population size function plugin.Also note that if you are dealing with a diploid population N0 will be the number of alleles, not the number of individuals. Population function for performing likelihood calculations based on Volz 2012.

beast.phylodynamics.epidemiology.SIR_Initializer => Initializes a stichastic SIR trajectory

beast.phylodynamics.epidemiology.SeasonalSIRSEpidemic => Plugin that performs calculations based on the State. Simulates a stochastic forward SIR, SEIR or SIRS epidemic Simulates a stochastic forward SIRS epidemic with seasonality

beast.phylodynamics.epidemiology.StochasticCoalescent => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule Calculates the probability of a beast.tree conditional on a population size function. Note that this does not take the number of possible tree interval/tree topology combinations in account, in other words, the constant required for making this a proper distribution that integrates to unity is not calculated (partly, because we don't know how for sequentially sampled data).

beast.phylodynamics.epidemiology.StochasticCoalescentSIR => Plugin that performs calculations based on the State. Keeps track of stochastic trajectories for effective, infected, and susceptible populations,used by SIRPopulationFunction

beast.phylodynamics.epidemiology.Volz2009TreeDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule Calculates the Volz-2009 probability of a beast.tree.

beast.phylogeography.RateIndicatorInitializer => RateIndicatorInitializer ported from BEAST1

beast.prevalence.AddOperator => Proposes a move in state space. Randomly adds Infection or recovery to prevalence list

beast.prevalence.DelOperator => Proposes a move in state space. Randomly removes Infection or recovery to prevalence list

beast.prevalence.MoveOperator => Proposes a move in state space. Randomly moves item in prevalence list

beast.prevalence.PrevalenceLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. likelihood of the prevalence sequence based on a set of parameters

beast.prevalence.PrevalenceList => Plugin that performs calculations based on the State. A node that can be part of the state. Prevalence list is a linked list with times and actions

beast.prevalence.SubtreeSlide => Proposes a move in state space. This operator changes a beast.tree. Moves the height of an internal node along the branch. If it moves up, it can exceed the root and become a new root. If it moves down, it may need to make a choise which branch to slide down into.

beast.prevalence.TreeForPrevalenceLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. likelihood of a tree conditioned on a prevalence sequence

beast.prevalence.TreeOperator not documented :null

beast.prevalence.TreeScaleOperator => Proposes a move in state space. This operator changes a beast.tree. Scales a complete beast.tree.

beast.prevalence.Uniform => Proposes a move in state space. This operator changes a beast.tree. Randomly selects true internal tree node (i.e. not the root) and move node height uniformly in interval restricted by the nodes parent and children.

beast.prevalence.WilsonBalding => Proposes a move in state space. This operator changes a beast.tree. Implements the unweighted Wilson-Balding branch swapping move. This move is similar to one proposed by WILSON and BALDING 1998 and involves removing a subtree and re-attaching it on a new parent branch. See <a href='http://www.genetics.org/cgi/content/full/161/3/1307/F1'>picture</a>.

beast.shell.BSHClockModel => Branch rate model specified using BEASTScript getRateForBranch(node, meanrate) must be specified.

beast.shell.BSHDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution specified using BEASTScript calculateLogP() must be specified.

beast.shell.BSHLogger => Logger specified using BEASTScript init(out), log(sample, out), close(out) must be specified.

beast.shell.BSHOperator => Proposes a move in state space. Operator specified using BEASTScript double proposal() must be specified.

beast.shell.BSHParametricDistribution => Plugin that performs calculations based on the State. A class that describes a parametric distribution, that is, a distribution that takes some parameters/valuables as inputs and can produce (cumulative) densities and inverse cumulative densities. Parmateric distribution (continuous, not integer) specified using BEASTScript desnity(x), cumulativeProbability(x) and inverseCumulativeProbability(p) must be specified.

beast.shell.BSHSiteModel => Sitemodel specified using BEASTScript getCategoryCount(), getCategoryOfSite(site, node), getRateForCategory(category, node), getCategoryRates(node), getProportionForCategory(category, node), getCategoryProportions(node) must be specified.

beast.shell.BSHSubstitutionModel => Substitution model specified using BEASTScript getTransitionProbabilities(node, fStartTime, fEndTime, fRate, matrix) must be specified.

beast.shell.BSHTreeDistribution => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Distribution on a tree, typically a prior such as Coalescent or Yule Substitution model specified using BEASTScript calculateLogP(tree, intervals) must be specified

beast.shell.NamedFunction => Plugin that performs calculations based on the State. Wraps a function in a name, so it can be identified in a BEASTShell script object

beast.util.ClusterTree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. Create initial beast.tree by hierarchical clustering, either through one of the classic link methods or by neighbor joining. The following link methods are supported: o single link, o complete link, o UPGMA=average link, o mean link, o centroid, o Ward and o adjusted complete link o neighborjoining o neighborjoining2 - corrects tree for tip data, unlike plain neighborjoining

beast.util.ClusterZBSATree => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. Create initial beast.tree by hierarchical clustering, either through one of the classic link methods or by neighbor joining. The following link methods are supported: o single link, o complete link, o UPGMA=average link, o mean link, o centroid, o Ward and o adjusted complete link o neighborjoining o neighborjoining2 - corrects tree for tip data, unlike plain neighborjoining

beast.util.Script => Plugin that performs calculations based on the State. Base class for Script-BEAST interoperation

beast.util.TreeParser => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. Create beast.tree by parsing from a specification of a beast.tree in Newick format (includes parsing of any meta data in the Newick string).

beast.util.ZeroBranchSATreeParser => Plugin that performs calculations based on the State. A node that can be part of the state. Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data. Create beast.tree by parsing from a specification of a beast.tree (which is a fake SA tree) in Newick format (includes parsing of any meta data in the Newick string).

snap.CoalescentUnitTreeLogger => Logs a tree with branch lengths 2*(branch length in SNAPP) / (theta value for branch)

snap.Data => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data Represents sequence data for SnAP analysis. The difference with standard sequence data is that constant sites are removed + 2 patterns are added at the end representing these constant sites, but with zero weight. The likelihood calculator deals with these different sites.

snap.GammaParameter => Plugin that performs calculations based on the State. A node that can be part of the state. A parameter represents a value in the state space that can be changed by operators. A real-valued parameter represents a value (or array of values if the dimension is larger than one) in the state space that can be changed by operators. Represents population size associated with each node in a tree.

snap.MCMC => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. Allow sampling from the prior.

snap.ML => Entry point for running a Beast task, for instance an MCMC or other probabilistic analysis, a simulation, etc. MCMC chain. This is the main element that controls which posterior to calculate, how long to run the chain and all other properties, which operators to apply on the state space and where to log results. Maximum likelihood search by hill climbing.

snap.NodeData => Nodes in building beast.tree data structure. This node has population parameter (coalescenceRate=2/theta) and some specific members for performing SnAP (SNP and AFLP) analysis.

snap.RateToTheta => Converts coalescence rates to thetas, using theta=2/coalescent rate

snap.SNPSequence => Single sequence in an alignment. A SNPSequence holds a collection of binary sequences that are summarized in a new sequence by counting the number of sites with a 1.

snap.ThetaLogger => Logger that reports coalescent rates as theta (using theta=2/rate)

snap.TreeLengthLogger => Logger to report sum of node heights of a tree

snap.TreeNodeLogger => Logger to report height of all internal nodes in a tree

snap.WeightedData => Plugin that performs calculations based on the State. Unordered set mapping keys to values Class representing alignment data Represents sequence data for SnAP analysis. The difference with standard sequence data is that constant sites are removed + 2 patterns are added at the end representing these constant sites, but with zero weight. The likelihood calculator deals with these different sites. Alignment with weights attached to patterns

snap.likelihood.SnAPPrior => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Standard prior for SnAP analysis, consisting of a Yule prior on the tree (parameterized by lambda) and gamma distribution over the theta values (with parameters alpha and beta). Thetas are represented by the coalescenceRate parameter where values are theta=2/coalescenceRate

snap.likelihood.SnAPTreeLikelihood => Plugin that performs calculations based on the State. Probabilistic representation that can produce a log probability for instance for running an MCMC chain. Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376. Implements a tree Likelihood Function for Single Site Sorted-sequences on a tree.

snap.likelihood.SnapSubstitutionModel =>

snap.operators.BudgerAndScaler => Proposes a move in state space. Randomly selects two nodes and swap them in the tree. Moves internal node height without changing the tree topology. So the range is limited by the height of the parent node and the height of the highest child. The gamma value is also scaled so that gamma*height is constant for all three branches

snap.operators.DelayedAcceptanceOperator => Proposes a move in state space. An operator that uses an approximate likelihood and filters out proposales with low acceptance based on the approximate likleihood

snap.operators.DelayedAcceptanceOperator$1 not documented :snap.operators.DelayedAcceptanceOperator$1

snap.operators.DelayedAcceptanceOperator$2 not documented :snap.operators.DelayedAcceptanceOperator$2

snap.operators.GammaMoveAll => Proposes a move in state space. Scales single value in gamma parameter.

snap.operators.GammaMover => Proposes a move in state space. Scales single value in gamma parameter.

snap.operators.MergeSplitSpeciesTree => Proposes a move in state space. This operator changes a beast.tree. Operator for merging and splitting branches of a species tree from Yang and Ranala PNAS 2010.

snap.operators.MutationMover => Proposes a move in state space. Operation that moves both U and V frequency parameters without changing the average rate

snap.operators.NodeBudger => Proposes a move in state space. Randomly selects two nodes and swap them in the tree. Moves internal node height without changing the tree topology. So the range is limited by the height of the parent node and the height of the highest child.

snap.operators.NodeSwapper => Proposes a move in state space. Randomly selects two nodes and swap them in the tree.

snap.operators.RateMixer => Proposes a move in state space. Moves length of branch and coalescence rate of branch in the opposit direction.

snap.operators.RootGammaMover => Proposes a move in state space. Scales value in gamma parameter associated with root node.

snap.operators.ScaleOperator => Proposes a move in state space. Scales a parameter or a complete beast.tree (depending on which of the two is specified.

...BeautiAlignmentProvider <= beast.app.beauti.BeautiAlignmentProvider

...BeautiConfig <= beast.app.beauti.BeautiConfig

...BeautiConnector <= beast.app.beauti.BeautiConnector

...BeautiDiscreteTraitProvider <= beast.app.beauti.BeautiDiscreteTraitProvider

...BeautiDoc <= beast.app.beauti.BeautiDoc

...BeautiLocationTraitProvider <= beast.app.beauti.BeautiLocationTraitProvider

...BeautiMorphModelAlignmentProvider <= beast.app.beauti.BeautiMorphModelAlignmentProvider

...BeautiPanelConfig <= beast.app.beauti.BeautiPanelConfig

...BeautiSLocationTraitProvider <= beast.app.beauti.BeautiSLocationTraitProvider

...BeautiSubTemplate <= beast.app.beauti.BeautiSubTemplate

...BEASTObjectSet <= beast.app.draw.BEASTObjectSet

...MergeDataWith <= beast.app.seqgen.MergeDataWith

...SequenceSimulator <= beast.app.seqgen.SequenceSimulator

...SimulatedAlignment <= beast.app.seqgen.SimulatedAlignment

...Plot <= beast.app.shell.Plot

...Series <= beast.app.shell.Series

..AbstractMultivariateTraitLikelihood <= beast.continuous.AbstractMultivariateTraitLikelihood

..FullyConjugateMultivariateTraitLikelihood <= beast.continuous.FullyConjugateMultivariateTraitLikelihood

..IntegratedMultivariateTraitLikelihood <= beast.continuous.IntegratedMultivariateTraitLikelihood

..MultivariateDiffusionModel <= beast.continuous.MultivariateDiffusionModel

..SampledMultivariateTraitLikelihood <= beast.continuous.SampledMultivariateTraitLikelihood

..BEASTObject <= beast.core.BEASTObject

..CalculationNode <= beast.core.CalculationNode

..DataNode <= beast.core.DataNode

..Distribution <= beast.core.Distribution

..FilteredValuable <= beast.core.FilteredValuable

..Likelihood <= beast.core.Likelihood

..Logger <= beast.core.Logger

..MCMC <= beast.core.MCMC

..MCMC2 <= beast.core.MCMC2

..Operator <= beast.core.Operator

..OperatorSchedule <= beast.core.OperatorSchedule

..Posterior <= beast.core.Posterior

..Runnable <= beast.core.Runnable

..State <= beast.core.State

..StateNode <= beast.core.StateNode

...BooleanParameter <= beast.core.parameter.BooleanParameter

...BooleanParameterList <= beast.core.parameter.BooleanParameterList

...CompoundValuable <= beast.core.parameter.CompoundValuable

...DPPointer <= beast.core.parameter.DPPointer

...DPValuable <= beast.core.parameter.DPValuable

...GeneralParameterList <= beast.core.parameter.GeneralParameterList

...IntegerParameter <= beast.core.parameter.IntegerParameter

...IntegerParameterList <= beast.core.parameter.IntegerParameterList

...InverseMatrixLogger <= beast.core.parameter.InverseMatrixLogger

...Map <= beast.core.parameter.Map

...Parameter$Base <= beast.core.parameter.Parameter$Base

...ParameterList <= beast.core.parameter.ParameterList

...ParameterMeanLogger <= beast.core.parameter.ParameterMeanLogger

...PointerMean <= beast.core.parameter.PointerMean

...QuietRealParameter <= beast.core.parameter.QuietRealParameter

...RealParameter <= beast.core.parameter.RealParameter

...RealParameterList <= beast.core.parameter.RealParameterList

...RealParameterWrapper <= beast.core.parameter.RealParameterWrapper

...CompoundDistribution <= beast.core.util.CompoundDistribution

...Count <= beast.core.util.Count

...ESS <= beast.core.util.ESS

...Indices <= beast.core.util.Indices

...LoggableSum <= beast.core.util.LoggableSum

...ParameterConstrainer <= beast.core.util.ParameterConstrainer

...PrintListIDNumber <= beast.core.util.PrintListIDNumber

...PrintPointerIDNumber <= beast.core.util.PrintPointerIDNumber

...Sum <= beast.core.util.Sum

...Alignment <= beast.evolution.alignment.Alignment

...AlignmentFromTrait <= beast.evolution.alignment.AlignmentFromTrait

...AlignmentFromTraitMap <= beast.evolution.alignment.AlignmentFromTraitMap

...AlignmentSubset <= beast.evolution.alignment.AlignmentSubset

...AscertainedAlignment <= beast.evolution.alignment.AscertainedAlignment

...Cognate <= beast.evolution.alignment.Cognate

...CognateAlignment <= beast.evolution.alignment.CognateAlignment

...FilteredAlignment <= beast.evolution.alignment.FilteredAlignment

...OldWVAlignment <= beast.evolution.alignment.OldWVAlignment

...PrunedAlignment <= beast.evolution.alignment.PrunedAlignment

...Sequence <= beast.evolution.alignment.Sequence

...Taxon <= beast.evolution.alignment.Taxon

...TaxonSet <= beast.evolution.alignment.TaxonSet

....Distance$Base <= beast.evolution.alignment.distance.Distance$Base

....F84Distance <= beast.evolution.alignment.distance.F84Distance

....HammingDistance <= beast.evolution.alignment.distance.HammingDistance

....JukesCantorDistance <= beast.evolution.alignment.distance.JukesCantorDistance

....SMMDistance <= beast.evolution.alignment.distance.SMMDistance

...BranchRateModel$Base <= beast.evolution.branchratemodel.BranchRateModel$Base

...RandomLocalClockModel <= beast.evolution.branchratemodel.RandomLocalClockModel

...RateStatistic <= beast.evolution.branchratemodel.RateStatistic

...StrictClockModel <= beast.evolution.branchratemodel.StrictClockModel

...SynchronizableUCRelaxedClock <= beast.evolution.branchratemodel.SynchronizableUCRelaxedClock

...UCRelaxedClockModel <= beast.evolution.branchratemodel.UCRelaxedClockModel

...Aminoacid <= beast.evolution.datatype.Aminoacid

...Binary <= beast.evolution.datatype.Binary

...ContinuousDataType <= beast.evolution.datatype.ContinuousDataType

...DataType$Base <= beast.evolution.datatype.DataType$Base

...IntegerData <= beast.evolution.datatype.IntegerData

...IntegerData2 <= beast.evolution.datatype.IntegerData2

...LanguageIntegerData <= beast.evolution.datatype.LanguageIntegerData

...LocationDataType <= beast.evolution.datatype.LocationDataType

...Nucleotide <= beast.evolution.datatype.Nucleotide

...StandardData <= beast.evolution.datatype.StandardData

...TwoStateCovarion <= beast.evolution.datatype.TwoStateCovarion

...UserDataType <= beast.evolution.datatype.UserDataType

...AncestralStateTreeLikelihood <= beast.evolution.likelihood.AncestralStateTreeLikelihood

...BeagleTreeLikelihood <= beast.evolution.likelihood.BeagleTreeLikelihood

...CompoundTempTreeLikelihood <= beast.evolution.likelihood.CompoundTempTreeLikelihood

...DPMultiAlignmentTreeLikelihood <= beast.evolution.likelihood.DPMultiAlignmentTreeLikelihood

...DPMultiTreesTreeLikelihood <= beast.evolution.likelihood.DPMultiTreesTreeLikelihood

...DPSepMultiTreesTreeLikelihood <= beast.evolution.likelihood.DPSepMultiTreesTreeLikelihood

...DPSepTreeLikelihood <= beast.evolution.likelihood.DPSepTreeLikelihood

...DPTreeLikelihood <= beast.evolution.likelihood.DPTreeLikelihood

...DummyDPSepTreeLikelihood <= beast.evolution.likelihood.DummyDPSepTreeLikelihood

...DummyDPTreeLikelihood <= beast.evolution.likelihood.DummyDPTreeLikelihood

...DummyTempTreeLikelihood <= beast.evolution.likelihood.DummyTempTreeLikelihood

...DummyTempWVTreeLikelihood <= beast.evolution.likelihood.DummyTempWVTreeLikelihood

...ExperimentalTreeLikelihood <= beast.evolution.likelihood.ExperimentalTreeLikelihood

...GenericTreeLikelihood <= beast.evolution.likelihood.GenericTreeLikelihood

...LeafTrait <= beast.evolution.likelihood.LeafTrait

...MixtureTreeLikelihood <= beast.evolution.likelihood.MixtureTreeLikelihood

...MultiAlignmentTempTreeLikelihood <= beast.evolution.likelihood.MultiAlignmentTempTreeLikelihood

...MultiAlignmentTempWVTreeLikelihood <= beast.evolution.likelihood.MultiAlignmentTempWVTreeLikelihood

...MultiTreesSepTempTreeLikelihood <= beast.evolution.likelihood.MultiTreesSepTempTreeLikelihood

...MultiTreesTempTreeLikelihood <= beast.evolution.likelihood.MultiTreesTempTreeLikelihood

...MultiTreesTempWVTreeLikelihood <= beast.evolution.likelihood.MultiTreesTempWVTreeLikelihood

...NewWVTreeLikelihood <= beast.evolution.likelihood.NewWVTreeLikelihood

...PartitionPositionLogger <= beast.evolution.likelihood.PartitionPositionLogger

...PartitionProvider <= beast.evolution.likelihood.PartitionProvider

...PartitionProviderByCodon <= beast.evolution.likelihood.PartitionProviderByCodon

...PartitionedTreeLikelihood <= beast.evolution.likelihood.PartitionedTreeLikelihood

...PointerLikelihood <= beast.evolution.likelihood.PointerLikelihood

...QuietTreeLikelihood <= beast.evolution.likelihood.QuietTreeLikelihood

...SepTempTreeLikelihood <= beast.evolution.likelihood.SepTempTreeLikelihood

...SepTempWVTreeLikelihood <= beast.evolution.likelihood.SepTempWVTreeLikelihood

...SlowDPSepTreeLikelihood <= beast.evolution.likelihood.SlowDPSepTreeLikelihood

...SlowDPTreeLikelihood <= beast.evolution.likelihood.SlowDPTreeLikelihood

...TempSiteTreeLikelihood <= beast.evolution.likelihood.TempSiteTreeLikelihood

...TempTreeLikelihood <= beast.evolution.likelihood.TempTreeLikelihood

...TempWVTreeLikelihood <= beast.evolution.likelihood.TempWVTreeLikelihood

...ThreadedTreeLikelihood <= beast.evolution.likelihood.ThreadedTreeLikelihood

...TraitedTreeLikelihood <= beast.evolution.likelihood.TraitedTreeLikelihood

...TreeLikelihood <= beast.evolution.likelihood.TreeLikelihood

...WVTreeLikelihood <= beast.evolution.likelihood.WVTreeLikelihood

...BitFlipBSSVSOperator <= beast.evolution.operators.BitFlipBSSVSOperator

...BitFlipOperator <= beast.evolution.operators.BitFlipOperator

...CategoricalPDirichletPriorSampler <= beast.evolution.operators.CategoricalPDirichletPriorSampler

...CategoryDeltaExchangeOperator <= beast.evolution.operators.CategoryDeltaExchangeOperator

...CombinedOperator <= beast.evolution.operators.CombinedOperator

...DeltaExchangeOperator <= beast.evolution.operators.DeltaExchangeOperator

...DirichletProcessPriorGibbsSampler <= beast.evolution.operators.DirichletProcessPriorGibbsSampler

...DirichletProcessPriorSampler <= beast.evolution.operators.DirichletProcessPriorSampler

...Exchange <= beast.evolution.operators.Exchange

...ExchangeForZeroBranchSampledAncestorTrees <= beast.evolution.operators.ExchangeForZeroBranchSampledAncestorTrees

...ExtendedRealRandomWalkOperator <= beast.evolution.operators.ExtendedRealRandomWalkOperator

...ExtendedUpDownOperator <= beast.evolution.operators.ExtendedUpDownOperator

...FasterRateDPPGibbsSampler <= beast.evolution.operators.FasterRateDPPGibbsSampler

...GeneralIntegerOperator <= beast.evolution.operators.GeneralIntegerOperator

...IntRandomWalkOperator <= beast.evolution.operators.IntRandomWalkOperator

...IntRandomWalkWithExclusion <= beast.evolution.operators.IntRandomWalkWithExclusion

...IntSwapWithExclusion <= beast.evolution.operators.IntSwapWithExclusion

...IntUniformOperator <= beast.evolution.operators.IntUniformOperator

...IntUniformWithExclusion <= beast.evolution.operators.IntUniformWithExclusion

...IntegerRandomWalkOperator <= beast.evolution.operators.IntegerRandomWalkOperator

...JointOperator <= beast.evolution.operators.JointOperator

...JumpToPoint <= beast.evolution.operators.JumpToPoint

...LeafToSampledAncestorJump <= beast.evolution.operators.LeafToSampledAncestorJump

...MeanMVNSampler <= beast.evolution.operators.MeanMVNSampler

...MultiPointerSwapOperator <= beast.evolution.operators.MultiPointerSwapOperator

...MultiScaleOperator <= beast.evolution.operators.MultiScaleOperator

...NetworkIntRandomWalkOperator <= beast.evolution.operators.NetworkIntRandomWalkOperator

...NodeReheight <= beast.evolution.operators.NodeReheight

...NtdBMADPPGibbsSampler <= beast.evolution.operators.NtdBMADPPGibbsSampler

...NtdBMAPointersSwapOperator <= beast.evolution.operators.NtdBMAPointersSwapOperator

...NtdBMARateDPPGibbsSampler <= beast.evolution.operators.NtdBMARateDPPGibbsSampler

...NtdBMARatePointersSwapOperator <= beast.evolution.operators.NtdBMARatePointersSwapOperator

...NtdBMARateSAMSPriorOperator <= beast.evolution.operators.NtdBMARateSAMSPriorOperator

...NtdBMASAMSPriorOperator <= beast.evolution.operators.NtdBMASAMSPriorOperator

...NtdBMASAMSRandomWalkOperator <= beast.evolution.operators.NtdBMASAMSRandomWalkOperator

...NtdBMASAMSTempOperator <= beast.evolution.operators.NtdBMASAMSTempOperator

...PLDeltaExchangeOperator <= beast.evolution.operators.PLDeltaExchangeOperator

...PLExtendedRealRandomWalkOperator <= beast.evolution.operators.PLExtendedRealRandomWalkOperator

...PLIntegerRandomWalkOperator <= beast.evolution.operators.PLIntegerRandomWalkOperator

...PLNetworkIntRandomWalkOperator <= beast.evolution.operators.PLNetworkIntRandomWalkOperator

...PLScaleOperator <= beast.evolution.operators.PLScaleOperator

...PickIndicatorOperator <= beast.evolution.operators.PickIndicatorOperator

...PrecisionMatrixGibbsOperator <= beast.evolution.operators.PrecisionMatrixGibbsOperator

...PrecisionWishartSampler <= beast.evolution.operators.PrecisionWishartSampler

...RBOperator <= beast.evolution.operators.RBOperator

...RBScaleOperator <= beast.evolution.operators.RBScaleOperator

...RateDPPGibbsSampler <= beast.evolution.operators.RateDPPGibbsSampler

...RatePointersSwapOperator <= beast.evolution.operators.RatePointersSwapOperator

...RateSAMSPriorOperator <= beast.evolution.operators.RateSAMSPriorOperator

...RealRandomWalkOperator <= beast.evolution.operators.RealRandomWalkOperator

...RegressionGibbsEffectOperator <= beast.evolution.operators.RegressionGibbsEffectOperator

...RegressionGibbsPrecisionOperator <= beast.evolution.operators.RegressionGibbsPrecisionOperator

...RestrictedSubtreeSlide <= beast.evolution.operators.RestrictedSubtreeSlide

...RootHeightScaleOperator <= beast.evolution.operators.RootHeightScaleOperator

...RootTraitRandowWalkOperator <= beast.evolution.operators.RootTraitRandowWalkOperator

...SAExchange <= beast.evolution.operators.SAExchange

...SAScaleOperator <= beast.evolution.operators.SAScaleOperator

...SAUniform <= beast.evolution.operators.SAUniform

...SAWilsonBalding <= beast.evolution.operators.SAWilsonBalding

...SampledNodeDateRandomWalker <= beast.evolution.operators.SampledNodeDateRandomWalker

...SampledNodeDateRandomWalkerForZeroBranchSATrees <= beast.evolution.operators.SampledNodeDateRandomWalkerForZeroBranchSATrees

...ScaleAndSlide <= beast.evolution.operators.ScaleAndSlide

...ScaleOffsetOperator <= beast.evolution.operators.ScaleOffsetOperator

...ScaleOperator <= beast.evolution.operators.ScaleOperator

...ScaleOperatorForZeroBranchSATrees <= beast.evolution.operators.ScaleOperatorForZeroBranchSATrees

...SliceOperator <= beast.evolution.operators.SliceOperator

...SpecificRealRandomWalkOperator <= beast.evolution.operators.SpecificRealRandomWalkOperator

...SphereRandomWalker <= beast.evolution.operators.SphereRandomWalker

...SubtreeSlide <= beast.evolution.operators.SubtreeSlide

...SwapOperator <= beast.evolution.operators.SwapOperator

...TipDatesRandomWalker <= beast.evolution.operators.TipDatesRandomWalker

...TipDatesScaler <= beast.evolution.operators.TipDatesScaler

...TraitGibbsOperator <= beast.evolution.operators.TraitGibbsOperator

...TreeDimensionJump <= beast.evolution.operators.TreeDimensionJump

...TreeOperator <= beast.evolution.operators.TreeOperator

...TreeWithMetaDataRandomWalker <= beast.evolution.operators.TreeWithMetaDataRandomWalker

...Uniform <= beast.evolution.operators.Uniform

...UniformForZeroBranchSATrees <= beast.evolution.operators.UniformForZeroBranchSATrees

...UniformOperator <= beast.evolution.operators.UniformOperator

...UpDownOperator <= beast.evolution.operators.UpDownOperator

...WilsonBalding <= beast.evolution.operators.WilsonBalding

...WilsonBaldingForZeroBranchSampledAncestorTrees <= beast.evolution.operators.WilsonBaldingForZeroBranchSampledAncestorTrees

...WilsonBaldingWithRateCategories <= beast.evolution.operators.WilsonBaldingWithRateCategories

....Vertex <= beast.evolution.operators.util.Vertex

...DPMultiAlignRateSiteModel <= beast.evolution.sitemodel.DPMultiAlignRateSiteModel

...DPMultiAlignSiteModel <= beast.evolution.sitemodel.DPMultiAlignSiteModel

...DPNtdRateSepSiteModel <= beast.evolution.sitemodel.DPNtdRateSepSiteModel

...DPNtdRateSiteModel <= beast.evolution.sitemodel.DPNtdRateSiteModel

...DPNtdSiteModel <= beast.evolution.sitemodel.DPNtdSiteModel

...DPRateSiteModel <= beast.evolution.sitemodel.DPRateSiteModel

...DPSingleAlignSiteModel <= beast.evolution.sitemodel.DPSingleAlignSiteModel

...DPSiteModel <= beast.evolution.sitemodel.DPSiteModel

...DefaultMixtureSiteModel <= beast.evolution.sitemodel.DefaultMixtureSiteModel

...DummySiteModel <= beast.evolution.sitemodel.DummySiteModel

...EfficientDPNtdRateSepSiteModel <= beast.evolution.sitemodel.EfficientDPNtdRateSepSiteModel

...GeneralJC69 <= beast.evolution.sitemodel.GeneralJC69

...MixtureSiteModel <= beast.evolution.sitemodel.MixtureSiteModel

...MixtureSubstModel <= beast.evolution.sitemodel.MixtureSubstModel

...QuietSiteModel <= beast.evolution.sitemodel.QuietSiteModel

...SiteModel <= beast.evolution.sitemodel.SiteModel

...SiteModelInterface$Base <= beast.evolution.sitemodel.SiteModelInterface$Base

...BirthDeathGernhard08Model <= beast.evolution.speciation.BirthDeathGernhard08Model

...BirthDeathSkylineModel <= beast.evolution.speciation.BirthDeathSkylineModel

...CalibratedBirthDeathModel <= beast.evolution.speciation.CalibratedBirthDeathModel

...CalibratedYuleInitialTree <= beast.evolution.speciation.CalibratedYuleInitialTree

...CalibratedYuleModel <= beast.evolution.speciation.CalibratedYuleModel

...CalibrationPoint <= beast.evolution.speciation.CalibrationPoint

...GeneTreeForSpeciesTreeDistribution <= beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution

...RandomGeneTree <= beast.evolution.speciation.RandomGeneTree

...RandomLocalYuleModel <= beast.evolution.speciation.RandomLocalYuleModel

...SABDSamplingThroughTimeModel <= beast.evolution.speciation.SABDSamplingThroughTimeModel

...SABirthDeathModel <= beast.evolution.speciation.SABirthDeathModel

...SpeciesTreeDistribution <= beast.evolution.speciation.SpeciesTreeDistribution

...SpeciesTreeLogger <= beast.evolution.speciation.SpeciesTreeLogger

...SpeciesTreePrior <= beast.evolution.speciation.SpeciesTreePrior

...StarBeastStartState <= beast.evolution.speciation.StarBeastStartState

...TreeTopFinder <= beast.evolution.speciation.TreeTopFinder

...UltrametricSpeciationModel <= beast.evolution.speciation.UltrametricSpeciationModel

...YuleModel <= beast.evolution.speciation.YuleModel

...YuleModelWithScaling <= beast.evolution.speciation.YuleModelWithScaling

...BinaryCovarion <= beast.evolution.substitutionmodel.BinaryCovarion

...Blosum62 <= beast.evolution.substitutionmodel.Blosum62

...CPREV <= beast.evolution.substitutionmodel.CPREV

...CladeSubstitutionModel <= beast.evolution.substitutionmodel.CladeSubstitutionModel

...ContinuousSubstitutionModel <= beast.evolution.substitutionmodel.ContinuousSubstitutionModel

...DPNtdBMA <= beast.evolution.substitutionmodel.DPNtdBMA

...Dayhoff <= beast.evolution.substitutionmodel.Dayhoff

...EmpiricalSubstitutionModel <= beast.evolution.substitutionmodel.EmpiricalSubstitutionModel

...EpochSubstitutionModel <= beast.evolution.substitutionmodel.EpochSubstitutionModel

...Frequencies <= beast.evolution.substitutionmodel.Frequencies

...GTR <= beast.evolution.substitutionmodel.GTR

...GeneralLazySubstitutionModel <= beast.evolution.substitutionmodel.GeneralLazySubstitutionModel

...GeneralSubstitutionModel <= beast.evolution.substitutionmodel.GeneralSubstitutionModel

...HKY <= beast.evolution.substitutionmodel.HKY

...JTT <= beast.evolution.substitutionmodel.JTT

...JukesCantor <= beast.evolution.substitutionmodel.JukesCantor

...LazyHKY <= beast.evolution.substitutionmodel.LazyHKY

...LewisMK <= beast.evolution.substitutionmodel.LewisMK

...MTREV <= beast.evolution.substitutionmodel.MTREV

...MutationDeathModel <= beast.evolution.substitutionmodel.MutationDeathModel

...NtdBMA <= beast.evolution.substitutionmodel.NtdBMA

...RB <= beast.evolution.substitutionmodel.RB

...SVSGeneralSubstitutionModel <= beast.evolution.substitutionmodel.SVSGeneralSubstitutionModel

...SubstitutionModel$Base <= beast.evolution.substitutionmodel.SubstitutionModel$Base

...SubstitutionModel$NucleotideBase <= beast.evolution.substitutionmodel.SubstitutionModel$NucleotideBase

...SwitchingNtdBMA <= beast.evolution.substitutionmodel.SwitchingNtdBMA

...TN93 <= beast.evolution.substitutionmodel.TN93

...VS <= beast.evolution.substitutionmodel.VS

...WAG <= beast.evolution.substitutionmodel.WAG

...Taxon <= beast.evolution.taxonomy.Taxon

...CladeConstraint <= beast.evolution.tree.CladeConstraint

...ConstrainedRandomTree <= beast.evolution.tree.ConstrainedRandomTree

...FlatMultiTypeTree <= beast.evolution.tree.FlatMultiTypeTree

...InitParamFromTree <= beast.evolution.tree.InitParamFromTree

...MigrationModel <= beast.evolution.tree.MigrationModel

...MonophyleticConstraint <= beast.evolution.tree.MonophyleticConstraint

...MultiTypeNode <= beast.evolution.tree.MultiTypeNode

...MultiTypeTree <= beast.evolution.tree.MultiTypeTree

...MultiTypeTreeFromNewick <= beast.evolution.tree.MultiTypeTreeFromNewick

...Node <= beast.evolution.tree.Node

...PrunedTree <= beast.evolution.tree.PrunedTree

...RandomMultiTypeTree <= beast.evolution.tree.RandomMultiTypeTree

...RandomTree <= beast.evolution.tree.RandomTree

...RootTrait <= beast.evolution.tree.RootTrait

...SALogger <= beast.evolution.tree.SALogger

...SATreeLogger <= beast.evolution.tree.SATreeLogger

...SampledAncestorLogger <= beast.evolution.tree.SampledAncestorLogger

...SamplingDate <= beast.evolution.tree.SamplingDate

...ScaledTreeHeightLogger <= beast.evolution.tree.ScaledTreeHeightLogger

...ScaledTreeWithMetaDataLogger <= beast.evolution.tree.ScaledTreeWithMetaDataLogger

...Scaler <= beast.evolution.tree.Scaler

...StructuredCoalescentMultiTypeTree <= beast.evolution.tree.StructuredCoalescentMultiTypeTree

...TraitSet <= beast.evolution.tree.TraitSet

...Tree <= beast.evolution.tree.Tree

...TreeDistribution <= beast.evolution.tree.TreeDistribution

...TreeHeightLogger <= beast.evolution.tree.TreeHeightLogger

...TreeHeightValuable <= beast.evolution.tree.TreeHeightValuable

...TreeLengthLogger <= beast.evolution.tree.TreeLengthLogger

...TreeReport <= beast.evolution.tree.TreeReport

...TreeScaler <= beast.evolution.tree.TreeScaler

...TreeTraitMap <= beast.evolution.tree.TreeTraitMap

...TreeTraitProvider$Helper <= beast.evolution.tree.TreeTraitProvider$Helper

...TreeWithMetaDataLogger <= beast.evolution.tree.TreeWithMetaDataLogger

...TreeWithTraitLogger <= beast.evolution.tree.TreeWithTraitLogger

...ZeroBranchSANode <= beast.evolution.tree.ZeroBranchSANode

...ZeroBranchSARandomTree <= beast.evolution.tree.ZeroBranchSARandomTree

...ZeroBranchSATree <= beast.evolution.tree.ZeroBranchSATree

....BayesianSkyline <= beast.evolution.tree.coalescent.BayesianSkyline

....CauchyPlusConstant <= beast.evolution.tree.coalescent.CauchyPlusConstant

....Coalescent <= beast.evolution.tree.coalescent.Coalescent

....CompoundPopulationFunction <= beast.evolution.tree.coalescent.CompoundPopulationFunction

....ConstantPopulation <= beast.evolution.tree.coalescent.ConstantPopulation

....ExponentialGrowth <= beast.evolution.tree.coalescent.ExponentialGrowth

....ExponentialGrowthPlusConstant <= beast.evolution.tree.coalescent.ExponentialGrowthPlusConstant

....PopulationFunction$Abstract <= beast.evolution.tree.coalescent.PopulationFunction$Abstract

....SampleOffValues <= beast.evolution.tree.coalescent.SampleOffValues

....ScaledPopulationFunction <= beast.evolution.tree.coalescent.ScaledPopulationFunction

....ScaledTreeIntervals <= beast.evolution.tree.coalescent.ScaledTreeIntervals

....StochasticCoalescentSkyline <= beast.evolution.tree.coalescent.StochasticCoalescentSkyline

....StructuredCoalescentTree <= beast.evolution.tree.coalescent.StructuredCoalescentTree

....TreeIntervals <= beast.evolution.tree.coalescent.TreeIntervals

..GeoSpatialDistribution <= beast.geo.GeoSpatialDistribution

..AbstractTreeDrawing <= beast.graphics.AbstractTreeDrawing

..ColorPlugin <= beast.graphics.ColorPlugin

..ColorTable <= beast.graphics.ColorTable

..NodeDecorator <= beast.graphics.NodeDecorator

..NodeDecorator$1 <= beast.graphics.NodeDecorator$1

..NodeTimesDecorator <= beast.graphics.NodeTimesDecorator

..RootedTreeDrawing <= beast.graphics.RootedTreeDrawing

..TreeDrawingGrid <= beast.graphics.TreeDrawingGrid

..UnrootedTreeDrawing <= beast.graphics.UnrootedTreeDrawing

..MCMCParticle <= beast.inference.MCMCParticle

..MCMCParticleAsync <= beast.inference.MCMCParticleAsync

..ML <= beast.inference.ML

..MultiMCMC <= beast.inference.MultiMCMC

..PairedPathSampleAnalyser <= beast.inference.PairedPathSampleAnalyser

..PairedPathSampler <= beast.inference.PairedPathSampler

..PairedPathSamplingStep <= beast.inference.PairedPathSamplingStep

..ParticleFilter <= beast.inference.ParticleFilter

..PathSampleAnalyser <= beast.inference.PathSampleAnalyser

..PathSampler <= beast.inference.PathSampler

..PathSamplerFromFile <= beast.inference.PathSamplerFromFile

..PathSamplingStep <= beast.inference.PathSamplingStep

..SimulatedAnnealing <= beast.inference.SimulatedAnnealing

...GeneralizedLinearModel <= beast.inference.distribution.GeneralizedLinearModel

...LinearRegression <= beast.inference.distribution.LinearRegression

...LogisticRegression <= beast.inference.distribution.LogisticRegression

...Beta <= beast.math.distributions.Beta

...CategoricalDistribution <= beast.math.distributions.CategoricalDistribution

...ChiSquare <= beast.math.distributions.ChiSquare

...CompoundDirichletProcess <= beast.math.distributions.CompoundDirichletProcess

...CompoundFossilPrior <= beast.math.distributions.CompoundFossilPrior

...ContinuousCategoricalDistribution <= beast.math.distributions.ContinuousCategoricalDistribution

...ContinuousCategoricalDistribution2 <= beast.math.distributions.ContinuousCategoricalDistribution2

...DegenerateBeta <= beast.math.distributions.DegenerateBeta

...DegenerateUniform <= beast.math.distributions.DegenerateUniform

...Dirichlet <= beast.math.distributions.Dirichlet

...DirichletDistribution <= beast.math.distributions.DirichletDistribution

...DirichletProcess <= beast.math.distributions.DirichletProcess

...DummyLikelihood <= beast.math.distributions.DummyLikelihood

...ExcludablePrior <= beast.math.distributions.ExcludablePrior

...Exponential <= beast.math.distributions.Exponential

...FossilCalibration <= beast.math.distributions.FossilCalibration

...FossilPrior <= beast.math.distributions.FossilPrior

...Gamma <= beast.math.distributions.Gamma

...IntegerUniformDistribution <= beast.math.distributions.IntegerUniformDistribution

...InverseGamma <= beast.math.distributions.InverseGamma

...LaplaceDistribution <= beast.math.distributions.LaplaceDistribution

...LogNormal <= beast.math.distributions.LogNormal

...LogNormalDistributionModel <= beast.math.distributions.LogNormalDistributionModel

...MRCAPrior <= beast.math.distributions.MRCAPrior

...MarkovChainDistribution <= beast.math.distributions.MarkovChainDistribution

...MultiMonophyleticConstraint <= beast.math.distributions.MultiMonophyleticConstraint

...Multinomial <= beast.math.distributions.Multinomial

...MultivariateNormal <= beast.math.distributions.MultivariateNormal

...MultivariateNormalDistribution <= beast.math.distributions.MultivariateNormalDistribution

...Normal <= beast.math.distributions.Normal

...NtdDP <= beast.math.distributions.NtdDP

...OneOnX <= beast.math.distributions.OneOnX

...ParameterListPrior <= beast.math.distributions.ParameterListPrior

...ParameterListsPrior <= beast.math.distributions.ParameterListsPrior

...ParametricDistribution <= beast.math.distributions.ParametricDistribution

...Poisson <= beast.math.distributions.Poisson

...Prior <= beast.math.distributions.Prior

...RBPrior <= beast.math.distributions.RBPrior

...SpecialMRCAPrior <= beast.math.distributions.SpecialMRCAPrior

...Uniform <= beast.math.distributions.Uniform

...UniformDistribution <= beast.math.distributions.UniformDistribution

...Wishart <= beast.math.distributions.Wishart

...WishartDistribution <= beast.math.distributions.WishartDistribution

...RPNcalculator <= beast.math.statistic.RPNcalculator

..BDSIR <= beast.phylodynamics.BDSIR

...CoalescentSIR <= beast.phylodynamics.epidemiology.CoalescentSIR

...CoalescentSimulator <= beast.phylodynamics.epidemiology.CoalescentSimulator

...CoalescentSimulatorBasic <= beast.phylodynamics.epidemiology.CoalescentSimulatorBasic

...CompoundSIROperator <= beast.phylodynamics.epidemiology.CompoundSIROperator

...DeterministicCoalescentSIR <= beast.phylodynamics.epidemiology.DeterministicCoalescentSIR

...HybridSEIREpidemic <= beast.phylodynamics.epidemiology.HybridSEIREpidemic

...HybridTrajectorySingleLocationSimulator <= beast.phylodynamics.epidemiology.HybridTrajectorySingleLocationSimulator

...SIRPopulationFunction <= beast.phylodynamics.epidemiology.SIRPopulationFunction

...SIR_Initializer <= beast.phylodynamics.epidemiology.SIR_Initializer

...SeasonalSIRSEpidemic <= beast.phylodynamics.epidemiology.SeasonalSIRSEpidemic

...StochasticCoalescent <= beast.phylodynamics.epidemiology.StochasticCoalescent

...StochasticCoalescentSIR <= beast.phylodynamics.epidemiology.StochasticCoalescentSIR

...Volz2009TreeDistribution <= beast.phylodynamics.epidemiology.Volz2009TreeDistribution

..RateIndicatorInitializer <= beast.phylogeography.RateIndicatorInitializer

..AddOperator <= beast.prevalence.AddOperator

..DelOperator <= beast.prevalence.DelOperator

..MoveOperator <= beast.prevalence.MoveOperator

..PrevalenceLikelihood <= beast.prevalence.PrevalenceLikelihood

..PrevalenceList <= beast.prevalence.PrevalenceList

..SubtreeSlide <= beast.prevalence.SubtreeSlide

..TreeForPrevalenceLikelihood <= beast.prevalence.TreeForPrevalenceLikelihood

..TreeOperator <= beast.prevalence.TreeOperator

..TreeScaleOperator <= beast.prevalence.TreeScaleOperator

..Uniform <= beast.prevalence.Uniform

..WilsonBalding <= beast.prevalence.WilsonBalding

..BSHClockModel <= beast.shell.BSHClockModel

..BSHDistribution <= beast.shell.BSHDistribution

..BSHLogger <= beast.shell.BSHLogger

..BSHOperator <= beast.shell.BSHOperator

..BSHParametricDistribution <= beast.shell.BSHParametricDistribution

..BSHSiteModel <= beast.shell.BSHSiteModel

..BSHSubstitutionModel <= beast.shell.BSHSubstitutionModel

..BSHTreeDistribution <= beast.shell.BSHTreeDistribution

..NamedFunction <= beast.shell.NamedFunction

..ClusterTree <= beast.util.ClusterTree

..ClusterZBSATree <= beast.util.ClusterZBSATree

..Script <= beast.util.Script

..TreeParser <= beast.util.TreeParser

..ZeroBranchSATreeParser <= beast.util.ZeroBranchSATreeParser

.CoalescentUnitTreeLogger <= snap.CoalescentUnitTreeLogger

.Data <= snap.Data

.GammaParameter <= snap.GammaParameter

.MCMC <= snap.MCMC

.ML <= snap.ML

.NodeData <= snap.NodeData

.RateToTheta <= snap.RateToTheta

.SNPSequence <= snap.SNPSequence

.ThetaLogger <= snap.ThetaLogger

.TreeLengthLogger <= snap.TreeLengthLogger

.TreeNodeLogger <= snap.TreeNodeLogger

.WeightedData <= snap.WeightedData

..SnAPPrior <= snap.likelihood.SnAPPrior

..SnAPTreeLikelihood <= snap.likelihood.SnAPTreeLikelihood

..SnapSubstitutionModel <= snap.likelihood.SnapSubstitutionModel

..BudgerAndScaler <= snap.operators.BudgerAndScaler

..DelayedAcceptanceOperator <= snap.operators.DelayedAcceptanceOperator

..DelayedAcceptanceOperator$1 <= snap.operators.DelayedAcceptanceOperator$1

..DelayedAcceptanceOperator$2 <= snap.operators.DelayedAcceptanceOperator$2

..GammaMoveAll <= snap.operators.GammaMoveAll

..GammaMover <= snap.operators.GammaMover

..MergeSplitSpeciesTree <= snap.operators.MergeSplitSpeciesTree

..MutationMover <= snap.operators.MutationMover

..NodeBudger <= snap.operators.NodeBudger

..NodeSwapper <= snap.operators.NodeSwapper

..RateMixer <= snap.operators.RateMixer

..RootGammaMover <= snap.operators.RootGammaMover

..ScaleOperator <= snap.operators.ScaleOperator

Page creation failed for beast.continuous.AbstractMultivariateTraitLikelihood: null

Page creation failed for beast.continuous.FullyConjugateMultivariateTraitLikelihood: beast.continuous.FullyConjugateMultivariateTraitLikelihood

Page creation failed for beast.continuous.IntegratedMultivariateTraitLikelihood: beast.continuous.IntegratedMultivariateTraitLikelihood

java.lang.ClassCastException: sun.reflect.generics.reflectiveObjects.ParameterizedTypeImpl cannot be cast to java.lang.Class

at beast.app.DocMaker.getType(Unknown Source)

at beast.app.DocMaker.getHTML(Unknown Source)

at beast.app.DocMaker.createPluginPage(Unknown Source)

at beast.app.DocMaker.generateDocs(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

Page creation failed for beast.core.BEASTObject: null

Page creation failed for beast.core.CalculationNode: null

Page creation failed for beast.core.Distribution: null

Page creation failed for beast.core.Operator: null

java.lang.TypeNotPresentException: Type beast.core.Prior not present

at sun.reflect.generics.factory.CoreReflectionFactory.makeNamedType(CoreReflectionFactory.java:117)

at sun.reflect.generics.visitor.Reifier.visitClassTypeSignature(Reifier.java:125)

at sun.reflect.generics.tree.ClassTypeSignature.accept(ClassTypeSignature.java:49)

at sun.reflect.generics.visitor.Reifier.reifyTypeArguments(Reifier.java:68)

at sun.reflect.generics.visitor.Reifier.visitClassTypeSignature(Reifier.java:138)

at sun.reflect.generics.tree.ClassTypeSignature.accept(ClassTypeSignature.java:49)

at sun.reflect.generics.repository.FieldRepository.getGenericType(FieldRepository.java:85)

at java.lang.reflect.Field.getGenericType(Field.java:241)

at beast.app.DocMaker.getType(Unknown Source)

at beast.app.DocMaker.getHTML(Unknown Source)

at beast.app.DocMaker.createPluginPage(Unknown Source)

at beast.app.DocMaker.generateDocs(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

Caused by: java.lang.ClassNotFoundException: beast.core.Prior

at java.net.URLClassLoader$1.run(URLClassLoader.java:372)

at java.net.URLClassLoader$1.run(URLClassLoader.java:361)

at java.security.AccessController.doPrivileged(Native Method)

at java.net.URLClassLoader.findClass(URLClassLoader.java:360)

at java.lang.ClassLoader.loadClass(ClassLoader.java:424)

at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)

at java.lang.ClassLoader.loadClass(ClassLoader.java:357)

at java.lang.Class.forName0(Native Method)

at java.lang.Class.forName(Class.java:344)

at sun.reflect.generics.factory.CoreReflectionFactory.makeNamedType(CoreReflectionFactory.java:114)

... 12 more

Page creation failed for beast.core.Runnable: null

Page creation failed for beast.core.StateNode: null

Page creation failed for beast.core.parameter.GeneralParameterList: null

Page creation failed for beast.core.parameter.Map: null

Page creation failed for beast.core.parameter.Parameter$Base: null

Page creation failed for beast.core.parameter.RealParameterWrapper: beast.core.parameter.RealParameterWrapper

Page creation failed for beast.evolution.alignment.OldWVAlignment: beast.evolution.alignment.OldWVAlignment

java.lang.ClassCastException: sun.reflect.generics.reflectiveObjects.ParameterizedTypeImpl cannot be cast to java.lang.Class

at beast.app.DocMaker.getType(Unknown Source)

at beast.app.DocMaker.getHTML(Unknown Source)

at beast.app.DocMaker.createPluginPage(Unknown Source)

at beast.app.DocMaker.generateDocs(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

Page creation failed for beast.evolution.branchratemodel.BranchRateModel$Base: null

Page creation failed for beast.evolution.datatype.DataType$Base: null

java.lang.ClassCastException: sun.reflect.generics.reflectiveObjects.ParameterizedTypeImpl cannot be cast to java.lang.Class

at beast.app.DocMaker.getType(Unknown Source)

at beast.app.DocMaker.getHTML(Unknown Source)

at beast.app.DocMaker.createPluginPage(Unknown Source)

at beast.app.DocMaker.generateDocs(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

java.lang.ClassCastException: sun.reflect.generics.reflectiveObjects.ParameterizedTypeImpl cannot be cast to java.lang.Class

at beast.app.DocMaker.getType(Unknown Source)

at beast.app.DocMaker.getHTML(Unknown Source)

at beast.app.DocMaker.createPluginPage(Unknown Source)

at beast.app.DocMaker.generateDocs(Unknown Source)

at beast.app.DocMaker.main(Unknown Source)

Page creation failed for beast.evolution.likelihood.TempSiteTreeLikelihood: beast.evolution.likelihood.TempSiteTreeLikelihood

Programmer error: input rule should be REQUIRED for this Input constructor (parameter)

Page creation failed for beast.evolution.operators.TreeOperator: null

Page creation failed for beast.evolution.sitemodel.DPMultiAlignSiteModel: null

Page creation failed for beast.evolution.sitemodel.DPSingleAlignSiteModel: null

Page creation failed for beast.evolution.sitemodel.DPSiteModel: null

Page creation failed for beast.evolution.sitemodel.QuietSiteModel: beast.evolution.sitemodel.QuietSiteModel

Page creation failed for beast.evolution.sitemodel.SiteModelInterface$Base: null

Programmer error: input rule should be REQUIRED for this Input constructor (relativeDeathRate)

Programmer error: input rule should be REQUIRED for this Input constructor (sampleProbability)

Page creation failed for beast.evolution.speciation.SpeciesTreeDistribution: null

Page creation failed for beast.evolution.speciation.UltrametricSpeciationModel: null

Page creation failed for beast.evolution.substitutionmodel.ContinuousSubstitutionModel: null

Page creation failed for beast.evolution.substitutionmodel.EmpiricalSubstitutionModel: null

Page creation failed for beast.evolution.substitutionmodel.SubstitutionModel$Base: null

Page creation failed for beast.evolution.substitutionmodel.SubstitutionModel$NucleotideBase: null

Page creation failed for beast.evolution.taxonomy.Taxon: beast.evolution.taxonomy.Taxon

Page creation failed for beast.evolution.tree.Scaler: null

Page creation failed for beast.evolution.tree.coalescent.PopulationFunction$Abstract: null

Page creation failed for beast.graphics.AbstractTreeDrawing: null

Page creation failed for beast.graphics.NodeDecorator$1: Class beast.app.DocMaker can not access a member of class beast.graphics.NodeDecorator$1 with modifiers ""

Programmer error: input rule should be REQUIRED for this Input constructor (model2)

Page creation failed for beast.math.distributions.ParametricDistribution: null

Page creation failed for beast.phylodynamics.epidemiology.CoalescentSIR: null

Page creation failed for beast.prevalence.TreeOperator: null

Page creation failed for snap.operators.DelayedAcceptanceOperator$1: snap.operators.DelayedAcceptanceOperator$1

Page creation failed for snap.operators.DelayedAcceptanceOperator$2: snap.operators.DelayedAcceptanceOperator$2

Done!!!

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