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  "Date/Publication": "2026-06-26 12:44:39 UTC",
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    "SplitConflicts",
    "SplitConsistent",
    "SplitFrequency",
    "SplitImbalance",
    "SplitInformation",
    "SplitMatchProbability",
    "SplitsInBinaryTree",
    "StarTree",
    "Stemminess",
    "StringToPhyDat",
    "Subsplit",
    "Subtree",
    "SupportColor",
    "SupportColour",
    "TCIContext",
    "TipLabels",
    "TipsInSplits",
    "TipTimedTree",
    "TntOrder",
    "TNTOrder",
    "TntText2Tree",
    "TNTText2Tree",
    "TopologyOnly",
    "TotalCopheneticIndex",
    "TreeIsRooted",
    "Treeness",
    "TreesMatchingSplit",
    "TreesMatchingTree",
    "TrivialSplits",
    "Unquote",
    "UnrootedKeys",
    "UnrootedTreeKey",
    "UnrootedTreeShape",
    "UnrootedTreesMatchingSplit",
    "UnrootedTreeWithKey",
    "UnrootedTreeWithShape",
    "UnrootTree",
    "UnshiftTree",
    "vapply64",
    "WithoutTrivialSplits",
    "WriteTntCharacters",
    "xor",
    "YuleTree",
    "ZeroTaxonTree"
  ],
  "_datasets": [
    {
      "name": "brewer",
      "title": "Brewer palettes",
      "object": "brewer",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "Lobo.data",
      "title": "Data from Zhang et al. 2016",
      "object": "Lobo",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "Lobo.phy",
      "title": "Data from Zhang et al. 2016",
      "object": "Lobo",
      "class": [
        "phyDat"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "nRootedShapes",
      "title": "Number of rooted / unrooted tree shapes",
      "object": "nRootedShapes",
      "class": [
        "integer64"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "nUnrootedShapes",
      "title": "Number of rooted / unrooted tree shapes",
      "object": "nUnrootedShapes",
      "class": [
        "integer64"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "unrootedKeys",
      "title": "Integer representing shape of a tree",
      "object": "unrootedKeys",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AddTip",
      "title": "Add a tip to a phylogenetic tree",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "AddTip",
        "AddTipEverywhere"
      ]
    },
    {
      "page": "ApeTime",
      "title": "Read modification time from \"ape\" Nexus file",
      "topics": [
        "ApeTime"
      ]
    },
    {
      "page": "ArtificialExtinction",
      "title": "Artificial Extinction",
      "topics": [
        "ArtEx",
        "ArtificialExtinction",
        "ArtificialExtinction.matrix",
        "ArtificialExtinction.phyDat"
      ]
    },
    {
      "page": "as.multiPhylo",
      "title": "Convert object to 'multiPhylo' class",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "as.multiPhylo",
        "as.multiPhylo.list",
        "as.multiPhylo.phyDat",
        "as.multiPhylo.phylo",
        "as.multiPhylo.Splits"
      ]
    },
    {
      "page": "as.Newick",
      "title": "Write a phylogenetic tree in Newick format",
      "topics": [
        "as.Newick",
        "as.Newick.list",
        "as.Newick.multiPhylo",
        "as.Newick.phylo"
      ]
    },
    {
      "page": "brewer",
      "title": "Brewer palettes",
      "topics": [
        "brewer"
      ]
    },
    {
      "page": "CharacterInformation",
      "title": "Character information content",
      "concept": [
        "split information functions"
      ],
      "topics": [
        "CharacterInformation"
      ]
    },
    {
      "page": "Cherries",
      "title": "Count cherries in a tree",
      "concept": [
        "tree properties"
      ],
      "topics": [
        "Cherries",
        "Cherries.numeric",
        "Cherries.phylo"
      ]
    },
    {
      "page": "CladeSizes",
      "title": "Clade sizes",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "CladeSizes"
      ]
    },
    {
      "page": "CladisticInfo",
      "title": "Cladistic information content of a tree",
      "concept": [
        "tree characterization functions",
        "tree information functions"
      ],
      "topics": [
        "CladisticInfo",
        "CladisticInfo.list",
        "CladisticInfo.multiPhylo",
        "CladisticInfo.phylo",
        "CladisticInfo.Splits",
        "CladisticInformation"
      ]
    },
    {
      "page": "ClusterTable",
      "title": "Convert phylogenetic tree to 'ClusterTable'",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "as.ClusterTable",
        "as.ClusterTable.list",
        "as.ClusterTable.multiPhylo",
        "as.ClusterTable.phylo",
        "ClusterTable"
      ]
    },
    {
      "page": "ClusterTable-methods",
      "title": "S3 methods for 'ClusterTable' objects",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "as.matrix.ClusterTable",
        "ClusterTable-methods",
        "print.ClusterTable",
        "summary.ClusterTable"
      ]
    },
    {
      "page": "CollapseNode",
      "title": "Collapse nodes on a phylogenetic tree",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "CollapseEdge",
        "CollapseNode",
        "CollapseNode.phylo"
      ]
    },
    {
      "page": "Consensus",
      "title": "Construct consensus trees",
      "concept": [
        "consensus tree functions",
        "tree characterization functions"
      ],
      "topics": [
        "Consensus"
      ]
    },
    {
      "page": "ConsensusWithout",
      "title": "Reduced consensus, omitting specified taxa",
      "concept": [
        "consensus tree functions",
        "tree manipulation",
        "tree properties"
      ],
      "topics": [
        "ConsensusWithout",
        "ConsensusWithout.list",
        "ConsensusWithout.multiPhylo",
        "ConsensusWithout.phylo",
        "MarkMissing"
      ]
    },
    {
      "page": "ConstrainedNJ",
      "title": "Constrained neighbour-joining tree",
      "concept": [
        "tree generation functions"
      ],
      "topics": [
        "ConstrainedNJ"
      ]
    },
    {
      "page": "Decompose",
      "title": "Decompose additive (ordered) phylogenetic characters",
      "concept": [
        "phylogenetic matrix conversion functions"
      ],
      "topics": [
        "Decompose"
      ]
    },
    {
      "page": "DescendantEdges",
      "title": "Identify descendant edges",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "DescendantEdges",
        "DescendantTips"
      ]
    },
    {
      "page": "DoubleFactorial",
      "title": "Double factorial",
      "concept": [
        "double factorials"
      ],
      "topics": [
        "DoubleFactorial",
        "DoubleFactorial64",
        "LnDoubleFactorial",
        "LnDoubleFactorial.int",
        "Log2DoubleFactorial",
        "LogDoubleFactorial",
        "LogDoubleFactorial.int"
      ]
    },
    {
      "page": "doubleFactorials",
      "title": "Double factorials",
      "concept": [
        "double factorials"
      ],
      "topics": [
        "doubleFactorials"
      ]
    },
    {
      "page": "DropTip",
      "title": "Drop leaves from tree",
      "concept": [
        "split manipulation functions",
        "tree manipulation"
      ],
      "topics": [
        "DropTip",
        "DropTip.list",
        "DropTip.multiPhylo",
        "DropTip.NULL",
        "DropTip.phylo",
        "DropTip.Splits",
        "DropTipPhylo",
        "KeepTip",
        "KeepTip.list",
        "KeepTip.multiPhylo",
        "KeepTip.NULL",
        "KeepTip.phylo",
        "KeepTip.Splits",
        "KeepTipPostorder",
        "KeepTipPreorder"
      ]
    },
    {
      "page": "edge_to_splits",
      "title": "Efficiently convert edge matrix to splits",
      "concept": [
        "C++ wrappers"
      ],
      "topics": [
        "edge_to_splits"
      ]
    },
    {
      "page": "EdgeAncestry",
      "title": "Ancestors of an edge",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "EdgeAncestry"
      ]
    },
    {
      "page": "EdgeDistances",
      "title": "Distance between edges",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "EdgeDistances"
      ]
    },
    {
      "page": "EdgeRatio",
      "title": "Ratio of external:internal edge length",
      "concept": [
        "tree properties"
      ],
      "topics": [
        "EdgeRatio",
        "EdgeRatio.phylo"
      ]
    },
    {
      "page": "EndSentence",
      "title": "Add full stop to end of a sentence",
      "concept": [
        "string parsing functions"
      ],
      "topics": [
        "EndSentence"
      ]
    },
    {
      "page": "GenerateTree",
      "title": "Generate pectinate, balanced or random trees",
      "concept": [
        "tree generation functions"
      ],
      "topics": [
        "BalancedTree",
        "GenerateTree",
        "PectinateTree",
        "RandomTree",
        "StarTree",
        "YuleTree"
      ]
    },
    {
      "page": "Hamming",
      "title": "Hamming distance between taxa in a phylogenetic dataset",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "Hamming"
      ]
    },
    {
      "page": "ImposeConstraint",
      "title": "Force a tree to match a constraint",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "AddUnconstrained",
        "ImposeConstraint"
      ]
    },
    {
      "page": "is.TreeNumber",
      "title": "Is an object a 'TreeNumber' object?",
      "concept": [
        "'TreeNumber' utilities"
      ],
      "topics": [
        "is.TreeNumber"
      ]
    },
    {
      "page": "J1Index",
      "title": "Robust universal tree balance index",
      "concept": [
        "tree characterization functions"
      ],
      "topics": [
        "J1Index",
        "JQIndex"
      ]
    },
    {
      "page": "KeptPaths",
      "title": "Paths present in reduced tree",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "KeptPaths",
        "KeptPaths.data.frame",
        "KeptPaths.matrix"
      ]
    },
    {
      "page": "KeptVerts",
      "title": "Identify vertices retained when leaves are dropped",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "KeptVerts",
        "KeptVerts.numeric",
        "KeptVerts.phylo"
      ]
    },
    {
      "page": "LabelSplits",
      "title": "Label splits",
      "concept": [
        "Splits operations"
      ],
      "topics": [
        "LabelSplits"
      ]
    },
    {
      "page": "LeafLabelInterchange",
      "title": "Leaf label interchange",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "LeafLabelInterchange"
      ]
    },
    {
      "page": "ListAncestors",
      "title": "List ancestors",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "AllAncestors",
        "ListAncestors"
      ]
    },
    {
      "page": "Lobo.data",
      "title": "Data from Zhang et al. 2016",
      "topics": [
        "Lobo.data",
        "Lobo.phy"
      ]
    },
    {
      "page": "logDoubleFactorials",
      "title": "Natural logarithms of double factorials",
      "concept": [
        "double factorials"
      ],
      "topics": [
        "logDoubleFactorials"
      ]
    },
    {
      "page": "LongBranch",
      "title": "Identify taxa with long branches",
      "concept": [
        "tree properties"
      ],
      "topics": [
        "LongBranch"
      ]
    },
    {
      "page": "MakeTreeBinary",
      "title": "Generate binary tree by collapsing polytomies",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "MakeTreeBinary"
      ]
    },
    {
      "page": "match.multiPhylo",
      "title": "Tree matching",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "%in%,multiPhylo,multiPhylo-method",
        "%in%,multiPhylo,phylo-method",
        "%in%,phylo,multiPhylo-method",
        "%in%,phylo,phylo-method",
        "match,multiPhylo,multiPhylo-method",
        "match,multiPhylo,phylo-method",
        "match,phylo,multiPhylo-method",
        "match,phylo,phylo-method"
      ]
    },
    {
      "page": "match.Splits",
      "title": "Split matching",
      "concept": [
        "Splits operations"
      ],
      "topics": [
        "%in%,Splits,Splits-method",
        "FirstMatchingSplit",
        "match",
        "match,Splits,Splits-method"
      ]
    },
    {
      "page": "MatchEdges",
      "title": "Match nodes and edges between trees",
      "concept": [
        "tree navigation",
        "tree properties"
      ],
      "topics": [
        "MatchEdges",
        "MatchNodes"
      ]
    },
    {
      "page": "MatchStrings",
      "title": "Check for mismatch between character vectors",
      "concept": [
        "string parsing functions"
      ],
      "topics": [
        "MatchStrings"
      ]
    },
    {
      "page": "MatrixToPhyDat",
      "title": "Convert between matrices and 'phyDat' objects",
      "concept": [
        "phylogenetic matrix conversion functions"
      ],
      "topics": [
        "MatrixToPhyDat",
        "PhyDatToMatrix"
      ]
    },
    {
      "page": "MorphoBankDecode",
      "title": "Decode MorphoBank text",
      "concept": [
        "string parsing functions"
      ],
      "topics": [
        "MorphoBankDecode"
      ]
    },
    {
      "page": "MRCA",
      "title": "Most recent common ancestor",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "MRCA"
      ]
    },
    {
      "page": "MSTEdges",
      "title": "Minimum spanning tree",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "MSTEdges",
        "MSTLength"
      ]
    },
    {
      "page": "N1Spr",
      "title": "Number of trees one SPR step away",
      "topics": [
        "IC1Spr",
        "N1Spr"
      ]
    },
    {
      "page": "NDescendants",
      "title": "Count descendants for each node in a tree",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "NDescendants"
      ]
    },
    {
      "page": "NewickTree",
      "title": "Write Newick Tree",
      "topics": [
        "NewickTree"
      ]
    },
    {
      "page": "NexusTokensToInteger",
      "title": "Convert Nexus token matrix to integer",
      "concept": [
        "phylogenetic matrix conversion functions"
      ],
      "topics": [
        "NexusTokensToInteger"
      ]
    },
    {
      "page": "NJTree",
      "title": "Generate a neighbour joining tree",
      "concept": [
        "tree generation functions"
      ],
      "topics": [
        "NJTree"
      ]
    },
    {
      "page": "NodeDepth",
      "title": "Distance of each node from tree exterior",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "NodeDepth"
      ]
    },
    {
      "page": "NodeNumbers",
      "title": "Numeric index of each node in a tree 'NodeNumbers()' returns a sequence corresponding to the nodes in a tree",
      "concept": [
        "tree navigation",
        "tree properties"
      ],
      "topics": [
        "NodeNumbers"
      ]
    },
    {
      "page": "NodeOrder",
      "title": "Number of edges incident to each node in a tree",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "NodeOrder"
      ]
    },
    {
      "page": "NPartitionPairs",
      "title": "Distributions of tips consistent with a partition pair",
      "topics": [
        "NPartitionPairs"
      ]
    },
    {
      "page": "NRooted",
      "title": "Number of trees",
      "concept": [
        "split information function",
        "tree information functions"
      ],
      "topics": [
        "LnRooted",
        "LnRooted.int",
        "LnUnrooted",
        "LnUnrooted.int",
        "LnUnrootedMult",
        "LnUnrootedSplits",
        "Log2Rooted",
        "Log2Rooted.int",
        "Log2Unrooted",
        "Log2Unrooted.int",
        "Log2UnrootedMult",
        "Log2UnrootedSplits",
        "NRooted",
        "NRooted64",
        "NUnrooted",
        "NUnrooted64",
        "NUnrootedMult",
        "NUnrootedSplits"
      ]
    },
    {
      "page": "nRootedShapes",
      "title": "Number of rooted / unrooted tree shapes",
      "topics": [
        "nRootedShapes",
        "nUnrootedShapes"
      ]
    },
    {
      "page": "NSplits",
      "title": "Number of distinct splits",
      "concept": [
        "Splits operations",
        "tree properties"
      ],
      "topics": [
        "NPartitions",
        "NSplits",
        "NSplits.character",
        "NSplits.ClusterTable",
        "NSplits.list",
        "NSplits.multiPhylo",
        "NSplits.NULL",
        "NSplits.numeric",
        "NSplits.phylo",
        "NSplits.Splits"
      ]
    },
    {
      "page": "NTip",
      "title": "Number of leaves in a phylogenetic tree",
      "concept": [
        "Splits operations",
        "tree properties"
      ],
      "topics": [
        "NTip",
        "NTip.default",
        "NTip.list",
        "NTip.matrix",
        "NTip.multiPhylo",
        "NTip.phyDat",
        "NTip.phylo",
        "NTip.Splits"
      ]
    },
    {
      "page": "PaintTree",
      "title": "Colour a tree by topology",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "PaintTree"
      ]
    },
    {
      "page": "PairwiseDistances",
      "title": "Distances between each pair of trees",
      "concept": [
        "pairwise tree distances"
      ],
      "topics": [
        "PairwiseDistances"
      ]
    },
    {
      "page": "PathLengths",
      "title": "Calculate length of paths between each pair of vertices within tree",
      "concept": [
        "tree properties"
      ],
      "topics": [
        "PathLengths"
      ]
    },
    {
      "page": "PolarizeSplits",
      "title": "Polarize splits on a single taxon",
      "concept": [
        "Splits operations"
      ],
      "topics": [
        "PolarizeSplits"
      ]
    },
    {
      "page": "print.TreeNumber",
      "title": "Print 'TreeNumber' object",
      "concept": [
        "'TreeNumber' utilities"
      ],
      "topics": [
        "print.TreeNumber"
      ]
    },
    {
      "page": "ReadCharacters",
      "title": "Read phylogenetic characters from file",
      "topics": [
        "PhyDat",
        "ReadAsPhyDat",
        "ReadCharacters",
        "ReadNotes",
        "ReadTNTAsPhyDat",
        "ReadTntAsPhyDat",
        "ReadTNTCharacters",
        "ReadTntCharacters"
      ]
    },
    {
      "page": "ReadMrBayesTrees",
      "title": "Read posterior tree sample produced by MrBayes",
      "concept": [
        "tree import functions"
      ],
      "topics": [
        "MrBayesTrees",
        "ReadMrBayes",
        "ReadMrBayesTrees"
      ]
    },
    {
      "page": "ReadTntTree",
      "title": "Parse TNT Tree",
      "concept": [
        "tree import functions"
      ],
      "topics": [
        "ReadTntTree",
        "TNTText2Tree",
        "TntText2Tree"
      ]
    },
    {
      "page": "Renumber",
      "title": "Renumber a tree's nodes and tips",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "Renumber"
      ]
    },
    {
      "page": "RenumberTips",
      "title": "Renumber a tree's tips",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "RenumberTips",
        "RenumberTips.list",
        "RenumberTips.multiPhylo",
        "RenumberTips.NULL",
        "RenumberTips.phylo",
        "RenumberTips.Splits"
      ]
    },
    {
      "page": "Reweight",
      "title": "Re-weight phylogenetic characters",
      "concept": [
        "phylogenetic matrix conversion functions"
      ],
      "topics": [
        "Reweight"
      ]
    },
    {
      "page": "RightmostCharacter",
      "title": "Rightmost character of string",
      "concept": [
        "string parsing functions"
      ],
      "topics": [
        "RightmostCharacter"
      ]
    },
    {
      "page": "RoguePlot",
      "title": "Visualize position of rogue taxa",
      "concept": [
        "consensus tree functions"
      ],
      "topics": [
        "RoguePlot"
      ]
    },
    {
      "page": "RootNode",
      "title": "Which node is a tree's root?",
      "concept": [
        "tree navigation"
      ],
      "topics": [
        "RootNode"
      ]
    },
    {
      "page": "RootTree",
      "title": "Root or unroot a phylogenetic tree",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "RootOnNode",
        "RootTree",
        "UnrootTree"
      ]
    },
    {
      "page": "SampleOne",
      "title": "Select element at random",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "SampleOne"
      ]
    },
    {
      "page": "sapply64",
      "title": "Apply a function that returns 64-bit integers over a list or vector",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "replicate64",
        "sapply64",
        "vapply64"
      ]
    },
    {
      "page": "sort.multiPhylo",
      "title": "Sort a list of phylogenetic trees",
      "concept": [
        "utility functions"
      ],
      "topics": [
        "<.MixedBase",
        "<.phylo",
        "==.MixedBase",
        "==.phylo",
        ">.MixedBase",
        ">.phylo",
        "sort.multiPhylo"
      ]
    },
    {
      "page": "SortTree",
      "title": "Sort tree",
      "concept": [
        "tree manipulation"
      ],
      "topics": [
        "SortTree",
        "SortTree.list",
        "SortTree.multiPhylo",
        "SortTree.phylo"
      ]
    },
    {
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