Package Index

API User's Guide  Class Hierarchy  Index

Other Packages

package corejava

package edu.stanford.ejalbert

package mesquite

package mesquite.ancstates.AncestralStatesAll

package mesquite.ancstates.LabelStatesOnTree

package mesquite.ancstates.RecAncestralStates

package mesquite.ancstates.ShadeStatesOnTree

package mesquite.ancstates.TraceAllCharacters

package mesquite.ancstates.TraceCharOverTrees

package mesquite.ancstates.TraceCharacterHistory

package mesquite.ancstates.aAncStatesIntro

package mesquite.assoc.ContainedAssociates

package mesquite.assoc.DepContTreeWindow

package mesquite.assoc.ManageAssociations

package mesquite.assoc.ManageDistributionBlock

package mesquite.assoc.PartitionFromAssociation

package mesquite.assoc.StoredAssociations

package mesquite.assoc.TaxonListAssoc

package mesquite.assoc.aAssocIntro

package mesquite.assoc.lib

package mesquite.basic.AssignTaxonNames

package mesquite.basic.CurrentTaxaPartition

package mesquite.basic.ExamplesNavigator

package mesquite.basic.GoToWebPage

package mesquite.basic.ManageFileComments

package mesquite.basic.ManageLabelsBlock

package mesquite.basic.ManageNotesBlock

package mesquite.basic.ManageSetsBlock

package mesquite.basic.ManageTaxaPartitions

package mesquite.basic.ManageTaxaSets

package mesquite.basic.NextProject

package mesquite.basic.RawNexusBlockEditor

package mesquite.basic.ShowText

package mesquite.basic.SuffixTaxonNames

package mesquite.basic.TaxaSelCoordinator

package mesquite.basic.TextWindowMaker

package mesquite.basic.TruncTaxonNames

package mesquite.batchArch.BatchTemplateManager

package mesquite.batchArch.ChartFromInstructions

package mesquite.batchArch.ExportMatricesBatch

package mesquite.batchArch.aBatchArchIntro

package mesquite.batchArch.lib

package mesquite.categ.ManageCategoricalChars

package mesquite.categ.ManageDNARNAChars

package mesquite.categ.ManageProteinChars

package mesquite.categ.StateNamesEditor

package mesquite.categ.lib

package mesquite.charMatrices.AddDeleteData

package mesquite.charMatrices.AlterData

package mesquite.charMatrices.BasicDataWindowCoord

package mesquite.charMatrices.BasicDataWindowMaker

package mesquite.charMatrices.BootstrapResample

package mesquite.charMatrices.CharMatrixCoordIndep

package mesquite.charMatrices.CharMatrixCoordObed

package mesquite.charMatrices.CharSelCoordinator

package mesquite.charMatrices.CharSrcCoordObed

package mesquite.charMatrices.ColorByFootnote

package mesquite.charMatrices.ColorByState

package mesquite.charMatrices.CompareMatrices

package mesquite.charMatrices.ConcatenateMatrices

package mesquite.charMatrices.DataPainter

package mesquite.charMatrices.DifferenceInNumsForChar

package mesquite.charMatrices.Fill

package mesquite.charMatrices.ManageAssumptionsBlock

package mesquite.charMatrices.ManageCharInclusion

package mesquite.charMatrices.ManageCharModels

package mesquite.charMatrices.ManageCharPartitions

package mesquite.charMatrices.ManageCharWeights

package mesquite.charMatrices.ManageCharacters

package mesquite.charMatrices.ManageCharsets

package mesquite.charMatrices.ManageCodonPositions

package mesquite.charMatrices.ManageCodonsBlock

package mesquite.charMatrices.ManageDATAblock

package mesquite.charMatrices.MatrixFromClipboard

package mesquite.charMatrices.MatrixSelection

package mesquite.charMatrices.NumForCharWithChar

package mesquite.charMatrices.PercentGaps

package mesquite.charMatrices.PercentMissing

package mesquite.charMatrices.QuickKeySelector

package mesquite.charMatrices.RandomFillCateg

package mesquite.charMatrices.RandomModifMatrix

package mesquite.charMatrices.RarefyMatrix

package mesquite.charMatrices.ReshuffleCharacter

package mesquite.charMatrices.ReshuffleMatrix

package mesquite.charMatrices.SaveMatrixCopies

package mesquite.charMatrices.SelectCharsWithProbP

package mesquite.charMatrices.SelectRndCharacters

package mesquite.charMatrices.SelectVariableCharacters

package mesquite.charMatrices.ShuffleStates

package mesquite.charMatrices.SortChar

package mesquite.charMatrices.SortTaxa

package mesquite.charMatrices.SprinkleMissing

package mesquite.charMatrices.StoredCharacters

package mesquite.charMatrices.StoredMatrices

package mesquite.charMatrices.Wand

package mesquite.charMatrices.WandChar

package mesquite.charMatrices.WandTaxon

package mesquite.charMatrices.aCharMatricesIntro

package mesquite.charMatrices.lib

package mesquite.charts.CharacterValuesChart

package mesquite.charts.CharsScattergram

package mesquite.charts.Histogram

package mesquite.charts.ItemValuesChart

package mesquite.charts.ItemsBiplot

package mesquite.charts.MatrixValuesChart

package mesquite.charts.NodesScattergram

package mesquite.charts.Scattergram

package mesquite.charts.ShowMean

package mesquite.charts.ShowPercentile

package mesquite.charts.ShowYEqualsX

package mesquite.charts.TaxaScattergram

package mesquite.charts.TaxonValuesChart

package mesquite.charts.TreeBlockValues

package mesquite.charts.TreeValuesChart

package mesquite.charts.TreesScattergram

package mesquite.coalesce.CoalescentTrees

package mesquite.coalesce.ContainedCoalescence

package mesquite.coalesce.DeepCoalMultLoci

package mesquite.coalesce.DeepCoalescencesG

package mesquite.coalesce.DeepCoalescencesSp

package mesquite.coalesce.InsertNode

package mesquite.coalesce.LineageWidth

package mesquite.coalesce.NeutralCoalescence

package mesquite.coalesce.RecCoalescenceHistory

package mesquite.coalesce.SlatkinMaddisonS

package mesquite.coalesce.TreeDepth

package mesquite.coalesce.aCoalescencePkgIntro

package mesquite.coalesce.lib

package mesquite.cont.AddItem

package mesquite.cont.AddNoise

package mesquite.cont.AddToStates

package mesquite.cont.ContinuousStatesT

package mesquite.cont.LogTransform

package mesquite.cont.ManageContChars

package mesquite.cont.MapContinuous

package mesquite.cont.MeanValue

package mesquite.cont.MultiplyStates

package mesquite.cont.NodeLocs2DPlot

package mesquite.cont.PlotTree

package mesquite.cont.RandomFillCont

package mesquite.cont.RemoveItem

package mesquite.cont.RenameItem

package mesquite.cont.Standardize

package mesquite.cont.lib

package mesquite.distance.AverageOfDistances

package mesquite.distance.ClusterAnalysis

package mesquite.distance.DistanceContainedTaxa

package mesquite.distance.PatristicDistance

package mesquite.distance.SingleLinkage

package mesquite.distance.TaxonDistance

package mesquite.distance.UPGMA

package mesquite.distance.UncorrectedDistance

package mesquite.distance.lib

package mesquite.genesis.CodePosRatesCurator

package mesquite.genesis.EvolveDNAChars

package mesquite.genesis.GammaCurator

package mesquite.genesis.GammaInvarCurator

package mesquite.genesis.InitDNASubmodels

package mesquite.genesis.InvarCurator

package mesquite.genesis.RateMatrixGTRCurator

package mesquite.genesis.RateMatrixTiTvCurator

package mesquite.genesis.SimDNAModelCurator

package mesquite.genesis.StateFreqDNAEmpCurator

package mesquite.genesis.StateFreqUserDNACurator

package mesquite.genesis.aGenesisIntro

package mesquite.genesis.lib

package mesquite.io.InterpretClustalDNA

package mesquite.io.InterpretClustalProtein

package mesquite.io.InterpretNBRFDNA

package mesquite.io.InterpretNBRFProtein

package mesquite.io.InterpretNonaHennig

package mesquite.io.InterpretPOYDNA

package mesquite.io.InterpretPhylipCat

package mesquite.io.InterpretPhylipDNA

package mesquite.io.InterpretPhylipProtein

package mesquite.io.InterpretSimpleCat

package mesquite.io.InterpretSimpleDNA

package mesquite.io.InterpretSimpleProtein

package mesquite.io.InterpretTabbedConts

package mesquite.io.aIOIntro

package mesquite.io.lib

package mesquite.jama.aJamaIntro

package mesquite.jsci.aJSciIntro

package mesquite.lib

package mesquite.lib.characters

package mesquite.lib.duties

package mesquite.lib.table

package mesquite.lists.CharInclSetList

package mesquite.lists.CharInclSetListNum

package mesquite.lists.CharListCodonPos

package mesquite.lists.CharListInclusion

package mesquite.lists.CharListPartition

package mesquite.lists.CharListWeights

package mesquite.lists.CharNumForList

package mesquite.lists.CharPartitionList

package mesquite.lists.CharSetList

package mesquite.lists.CharSetListNum

package mesquite.lists.CharacterList

package mesquite.lists.CharacterStats

package mesquite.lists.CodePosSetsList

package mesquite.lists.DatasetList

package mesquite.lists.DatasetsListClass

package mesquite.lists.DatasetsListNumChars

package mesquite.lists.DatasetsListTaxa

package mesquite.lists.ModelsList

package mesquite.lists.ModelsListDatatype

package mesquite.lists.ModelsListParadigm

package mesquite.lists.ModelsListType

package mesquite.lists.ModelsListWhole

package mesquite.lists.NexusBlockList

package mesquite.lists.NumForCharMatrixList

package mesquite.lists.NumForTaxaList

package mesquite.lists.NumForTreeList

package mesquite.lists.NumForTreeblockList

package mesquite.lists.TaxaPartListNumGroups

package mesquite.lists.TaxaPartitionList

package mesquite.lists.TaxaSetListNum

package mesquite.lists.TaxablockList

package mesquite.lists.TaxablockListNumber

package mesquite.lists.TaxonList

package mesquite.lists.TaxonListCurrPartition

package mesquite.lists.TaxonSetList

package mesquite.lists.TreeListAttachment

package mesquite.lists.TreeListPolyAssumption

package mesquite.lists.TreeListPolys

package mesquite.lists.TreeListRooted

package mesquite.lists.TreeblockList

package mesquite.lists.TreeblocksListNumber

package mesquite.lists.TreeblocksListTaxa

package mesquite.lists.TreesList

package mesquite.lists.WeightSetList

package mesquite.lists.lib

package mesquite.minimal.BasicFileCoordinator

package mesquite.minimal.Defaults

package mesquite.minimal.DrawHierarchy

package mesquite.minimal.InterpretNEXUS

package mesquite.minimal.ManageForeignBlocks

package mesquite.minimal.ManageMesquiteBlock

package mesquite.minimal.ManageTaxa

package mesquite.minimal.NEXUSDefaults

package mesquite.minimal.ShowEmployeeTree

package mesquite.minimal.StoredTaxa

package mesquite.minimal.WindowBabysitter

package mesquite.molec.AAHydrophobicity

package mesquite.molec.AASize

package mesquite.molec.AminoAcidProperties

package mesquite.molec.CharacterGCBias

package mesquite.molec.ColorByNumber

package mesquite.molec.CompareBasesWithTaxon

package mesquite.molec.GCAsNumber

package mesquite.molec.MeanValueLinked

package mesquite.molec.NucleotideComplement

package mesquite.molec.PercentMissingInTaxon

package mesquite.molec.PercentPolymorphic

package mesquite.molec.ReverseSequence

package mesquite.molec.SiteProperty

package mesquite.molec.TaxonGCBias

package mesquite.molec.lib

package mesquite.ornamental.BranchNotes

package mesquite.ornamental.CircularTree

package mesquite.ornamental.Constellation

package mesquite.ornamental.ManageHyperlinks

package mesquite.ornamental.ManagePictures

package mesquite.ornamental.NodeLocsCircular

package mesquite.ornamental.NodeLocsOval

package mesquite.ornamental.NodeNumbers

package mesquite.ornamental.NodePositionAdjust

package mesquite.ornamental.PictureWindowMaker

package mesquite.ornamental.Projector

package mesquite.ornamental.TaxonLink

package mesquite.pairwise.PairsNoChars

package mesquite.pairwise.PairsOneChar

package mesquite.pairwise.PairsTwoChars

package mesquite.pairwise.PairwiseComparison

package mesquite.pairwise.aPairwiseIntro

package mesquite.pairwise.lib

package mesquite.pal.aPALIntro

package mesquite.parsimony.CharListParsModels

package mesquite.parsimony.CharStepsDifference

package mesquite.parsimony.CurrentParsModels

package mesquite.parsimony.InitCategParsimony

package mesquite.parsimony.InitContParsimony

package mesquite.parsimony.InitializeParsimony

package mesquite.parsimony.ManageTypesets

package mesquite.parsimony.ParsAncestralStates

package mesquite.parsimony.ParsCharSteps

package mesquite.parsimony.ParsimonyCostMatrix

package mesquite.parsimony.ParsimonyLinear

package mesquite.parsimony.ParsimonyOrdered

package mesquite.parsimony.ParsimonySquared

package mesquite.parsimony.ParsimonyUnordered

package mesquite.parsimony.StepMatrixCurator

package mesquite.parsimony.StepsInCharacter

package mesquite.parsimony.StoredParsModel

package mesquite.parsimony.Treelength

package mesquite.parsimony.TreelengthForMatrix

package mesquite.parsimony.TypesetList

package mesquite.parsimony.aParsimonyIntro

package mesquite.parsimony.lib

package mesquite.rhetenor.CanonicalVariates

package mesquite.rhetenor.CharFromOrdinations

package mesquite.rhetenor.CharLoadings

package mesquite.rhetenor.CharsFromMatrices

package mesquite.rhetenor.EvolutionaryPCA

package mesquite.rhetenor.LandmarkDrawings

package mesquite.rhetenor.MatricesFromOrdinations

package mesquite.rhetenor.NodeLocs3DPlot

package mesquite.rhetenor.PlotTree3D

package mesquite.rhetenor.PrincipalComponents

package mesquite.rhetenor.ShowCharLoadings

package mesquite.rhetenor.aPCA

package mesquite.rhetenor.aRhetenorIntro

package mesquite.rhetenor.lib

package mesquite.rhetenor.wPCA

package mesquite.search.AddAndRearrange

package mesquite.search.NNIRearranger

package mesquite.search.SPRRearranger

package mesquite.search.TreeSearch

package mesquite.search.aSearchIntro

package mesquite.stochchar.AsymmModelCurator

package mesquite.stochchar.AsymmetryLR

package mesquite.stochchar.Brownian

package mesquite.stochchar.CharLikelihood

package mesquite.stochchar.CharListProbModels

package mesquite.stochchar.CurrentProbModels

package mesquite.stochchar.EvolveCategChars

package mesquite.stochchar.EvolveContinuous

package mesquite.stochchar.GainLossRates

package mesquite.stochchar.InterpretPagelFormat

package mesquite.stochchar.InterpretPagelFormatM

package mesquite.stochchar.LikelihoodInCharacter

package mesquite.stochchar.ManageCharModelsBlock

package mesquite.stochchar.ManageProbModelSets

package mesquite.stochchar.MargProbAncStates

package mesquite.stochchar.Mk1Rate

package mesquite.stochchar.MkModelCurator

package mesquite.stochchar.ProbModelSetList

package mesquite.stochchar.SimAncestralStates

package mesquite.stochchar.SimMatricesOnTrees

package mesquite.stochchar.SimulatedCharacters

package mesquite.stochchar.SimulatedMatrix

package mesquite.stochchar.StoredProbModel

package mesquite.stochchar.StoredProbModelSim

package mesquite.stochchar.aStochCharIntro

package mesquite.stochchar.lib

package mesquite.stochchar.zMargLikeCateg

package mesquite.treefarm.AllDichotomousTrees

package mesquite.treefarm.AllRerootings

package mesquite.treefarm.AugmentTreeRandomly

package mesquite.treefarm.CollessImbalance

package mesquite.treefarm.CompareOtherTree

package mesquite.treefarm.CompareOtherTrees

package mesquite.treefarm.ConcatTreeBlocks

package mesquite.treefarm.ConsensusTree

package mesquite.treefarm.DeleteReticulations

package mesquite.treefarm.DetermModifTree

package mesquite.treefarm.EqualRatesSpSampled

package mesquite.treefarm.ExtractTreeBlock

package mesquite.treefarm.MakeRerootings

package mesquite.treefarm.NoiseToBranchLengths

package mesquite.treefarm.RandomBranchMoves

package mesquite.treefarm.RandomModifTree

package mesquite.treefarm.RandomResolve

package mesquite.treefarm.RandomlyModifiedTrees

package mesquite.treefarm.RarefyTree

package mesquite.treefarm.RearrangedTree

package mesquite.treefarm.ReshuffleTaxa

package mesquite.treefarm.SharedPartitions2Trees

package mesquite.treefarm.TerminalInstability

package mesquite.treefarm.aTreeFarmIntro

package mesquite.treefarm.lib

package mesquite.trees.AddTaxaToTree

package mesquite.trees.AllBranchLengthsOne

package mesquite.trees.AllUnassignBrLengths1

package mesquite.trees.ArcTree

package mesquite.trees.AverageTreeValue

package mesquite.trees.BallsNSticks

package mesquite.trees.BasicDrawTaxonNames

package mesquite.trees.BasicTreeDrawCoordinator

package mesquite.trees.BasicTreeWindowCoord

package mesquite.trees.BasicTreeWindowMaker

package mesquite.trees.BranchInfo

package mesquite.trees.BranchLengthsAdjust

package mesquite.trees.CollapseZeroToPolys

package mesquite.trees.ColorBranches

package mesquite.trees.DeassignBranchLengths

package mesquite.trees.DefaultTrees

package mesquite.trees.DependentTreeWindow

package mesquite.trees.DiagonalDrawTree

package mesquite.trees.EqualRatesMarkovSp

package mesquite.trees.EquiprobableTrees

package mesquite.trees.LabelBranchLengths

package mesquite.trees.ListedTreeBlocks

package mesquite.trees.ManageTrees

package mesquite.trees.MirrorTreeWindowMaker

package mesquite.trees.MultiTreeWindowMaker

package mesquite.trees.NegativeToZeroBL

package mesquite.trees.NodeLocsStandard

package mesquite.trees.NodeNamer

package mesquite.trees.NumFor2CharCurrentTree

package mesquite.trees.NumForCharCurrentTree

package mesquite.trees.NumForCharOnTree

package mesquite.trees.NumForMatCurrentTree

package mesquite.trees.NumForTreeWith2Chars

package mesquite.trees.NumForTreeWithChar

package mesquite.trees.NumberOfTaxa

package mesquite.trees.OtherTreeBlocks

package mesquite.trees.ResolvePolytomiesToZero

package mesquite.trees.ScaleBranchLengths

package mesquite.trees.ScaleSelBranchLengths

package mesquite.trees.SelectBranches

package mesquite.trees.SelectTaxaInClade

package mesquite.trees.SetAssumptionDefault

package mesquite.trees.SetAssumptionHard

package mesquite.trees.SetAssumptionSoft

package mesquite.trees.SetBranchLengths

package mesquite.trees.SetPolytomyDefault

package mesquite.trees.SetSelBranchLengths

package mesquite.trees.SetToRooted

package mesquite.trees.SetToUnrooted

package mesquite.trees.ShadeNumbersOnTree

package mesquite.trees.SimulateTree

package mesquite.trees.SimulatedTreeBlocks

package mesquite.trees.SquareTree

package mesquite.trees.StoredTreeBlocks

package mesquite.trees.StoredTrees

package mesquite.trees.TreeLegendMaker

package mesquite.trees.TreeNotesMaker

package mesquite.trees.TreeOfContext

package mesquite.trees.TreeValueUsingMatrix

package mesquite.trees.Ultrametricize

package mesquite.trees.ValuesAtNodes

package mesquite.trees.aTreesIntro

package mesquite.trunk