API for TreeTools
Create, Modify and Analyse Phylogenetic Trees
| Global functions | |
|---|---|
| %in%,Splits,Splits-method | Man page |
| .AddRootRow | Source code |
| .AllAncestors | Source code |
| .AllDescendantEdges | Source code |
| .AncestorTable | Source code |
| .BalancedBit | Source code |
| .Comparable | Source code |
| .CompatibleRaws | Man page Source code |
| .CompatibleSplit | Man page Source code |
| .Depth | Source code |
| .DescendantTips | Source code |
| .Edge | Source code |
| .Edge.list | Source code |
| .Edge.numeric | Source code |
| .Edge.phylo | Source code |
| .EnforceOutgroup | Source code |
| .FindRoot | Source code |
| .GetAdjacency | Source code |
| .GetSubtreeSizes | Source code |
| .Int64 | Source code |
| .Int64.to.C | Source code |
| .ListDescendants | Source code |
| .ListLabels | Source code |
| .LogUTMS | Source code |
| .MCI | Source code |
| .MaskSplits | Source code |
| .MoveUp | Source code |
| .NodeDepth.rooted | Source code |
| .NodeDescendants | Source code |
| .PhyDatWithContrast | Source code |
| .PreorderTree | Source code |
| .PrintNUnrooted | Source code |
| .PrintedTreeNumber | Source code |
| .RandomParent | Man page Source code |
| .ReadMrBayesTrees | Source code |
| .RegExpMatches | Source code |
| .Sortable | Source code |
| .SubsetPhyDat | Source code |
| .TextToTree | Source code |
| .TntCommands | Source code |
| .UTFLines | Source code |
| .UnescapeQuotes | Source code |
| .UnrootedKeys | Man page Source code |
| .UpdateNodeLabel | Source code |
| .UpdateNodeLabel.numeric | Source code |
| .UpdateNodeLabel.phylo | Source code |
| .apply | Source code |
| .in.Splits | Source code |
| .onUnload | Source code |
| .vapply | Source code |
| <.MixedBase | Man page |
| <.phylo | Man page |
| ==.MixedBase | Man page |
| ==.phylo | Man page |
| >.MixedBase | Man page |
| >.phylo | Man page |
| AddTip | Man page Source code |
| AddTipEverywhere | Man page Source code |
| AddUnconstrained | Man page Source code |
| AllAncestors | Man page Source code |
| AllDescendantEdges | Man page Source code |
| AllTipLabels | Man page Source code |
| AllTipLabels.Splits | Man page Source code |
| AllTipLabels.TreeNumber | Man page Source code |
| AllTipLabels.list | Man page Source code |
| AllTipLabels.matrix | Man page Source code |
| AllTipLabels.multiPhylo | Man page |
| AllTipLabels.phylo | Man page Source code |
| AncestorEdge | Man page Source code |
| ApePostorder | Man page Source code |
| ApePostorder.NULL | Man page Source code |
| ApePostorder.list | Man page Source code |
| ApePostorder.multiPhylo | Man page Source code |
| ApePostorder.phylo | Man page Source code |
| ApeTime | Man page Source code |
| ArtEx | Man page |
| ArtificialExtinction | Man page Source code |
| ArtificialExtinction.matrix | Man page Source code |
| ArtificialExtinction.phyDat | Man page Source code |
| BalancedTree | Man page Source code |
| CharacterInformation | Man page Source code |
| CladeSizes | Man page Source code |
| Cladewise | Man page Source code |
| Cladewise.NULL | Man page Source code |
| Cladewise.list | Man page Source code |
| Cladewise.matrix | Man page Source code |
| Cladewise.multiPhylo | Man page Source code |
| Cladewise.phylo | Man page Source code |
| CladisticInfo | Man page Source code |
| CladisticInfo.Splits | Man page Source code |
| CladisticInfo.list | Man page Source code |
| CladisticInfo.multiPhylo | Man page |
| CladisticInfo.phylo | Man page Source code |
| CladisticInformation | Man page |
| ClusterTable | Man page |
| ClusterTable-methods | Man page |
| ClusterTable_decode | Source code |
| ClusterTable_matrix | Source code |
| ClusterTable_new | Source code |
| CollapseEdge | Man page Source code |
| CollapseNode | Man page Source code |
| CollapseNode.phylo | Man page Source code |
| CompatibleSplits | Man page Source code |
| Consensus | Man page Source code |
| ConsensusWithout | Man page Source code |
| ConsensusWithout.list | Man page |
| ConsensusWithout.multiPhylo | Man page Source code |
| ConsensusWithout.phylo | Man page Source code |
| ConstrainedNJ | Man page Source code |
| DescendantEdges | Man page Source code |
| DescendantTips | Man page Source code |
| DoubleFactorial | Man page Source code |
| DoubleFactorial64 | Man page Source code |
| DropTip | Man page Source code |
| DropTip.NULL | Man page Source code |
| DropTip.Splits | Man page Source code |
| DropTip.list | Man page Source code |
| DropTip.multiPhylo | Man page Source code |
| DropTip.phylo | Man page Source code |
| DropTipPhylo | Man page |
| EdgeAncestry | Man page Source code |
| EdgeDistances | Man page Source code |
| EndSentence | Man page Source code |
| EnforceOutgroup | Man page Source code |
| EnforceOutgroup.character | Man page Source code |
| EnforceOutgroup.phylo | Man page Source code |
| ExtractTaxa | Man page Source code |
| ForestSplits | Man page Source code |
| GenerateTree | Man page |
| Hamming | Man page Source code |
| IC1Spr | Man page Source code |
| ImposeConstraint | Man page Source code |
| J1Index | Man page Source code |
| JQIndex | Man page |
| KeepTip | Man page Source code |
| KeepTipPostorder | Man page Source code |
| KeepTipPreorder | Man page Source code |
| KeptPaths | Man page Source code |
| KeptPaths.data.frame | Man page Source code |
| KeptPaths.matrix | Man page Source code |
| KeptVerts | Man page Source code |
| KeptVerts.numeric | Man page Source code |
| KeptVerts.phylo | Man page Source code |
| LabelSplits | Man page Source code |
| LeafLabelInterchange | Man page Source code |
| ListAncestors | Man page Source code |
| LnDoubleFactorial | Man page |
| LnDoubleFactorial.int | Man page Source code |
| LnRooted | Man page Source code |
| LnRooted.int | Man page Source code |
| LnSplitMatchProbability | Man page Source code |
| LnTreesMatchingSplit | Man page Source code |
| LnTreesMatchingTree | Man page Source code |
| LnUnrooted | Man page Source code |
| LnUnrooted.int | Man page Source code |
| LnUnrootedMult | Man page Source code |
| LnUnrootedSplits | Man page Source code |
| LnUnrootedTreesMatchingSplit | Man page Source code |
| Lobo.data | Man page |
| Lobo.phy | Man page |
| Log2DoubleFactorial | Man page |
| Log2Rooted | Man page Source code |
| Log2Rooted.int | Man page Source code |
| Log2TreesMatchingSplit | Man page Source code |
| Log2TreesMatchingTree | Man page Source code |
| Log2Unrooted | Man page Source code |
| Log2Unrooted.int | Man page Source code |
| Log2UnrootedMult | Man page Source code |
| Log2UnrootedSplits | Man page Source code |
| Log2UnrootedTreesMatchingSplit | Man page Source code |
| LogDoubleFactorial | Man page |
| LogDoubleFactorial.int | Man page |
| MRCA | Man page Source code |
| MSTEdges | Man page Source code |
| MSTLength | Man page Source code |
| MakeTreeBinary | Man page Source code |
| MakeTreeBinary.list | Source code |
| MakeTreeBinary.multiPhylo | Source code |
| MakeTreeBinary.phylo | Source code |
| MarkMissing | Man page Source code |
| MatchEdges | Man page Source code |
| MatchNodes | Man page Source code |
| MatrixToPhyDat | Man page Source code |
| MinimumSpanningTree | Source code |
| MinimumSpanningTree.dist | Source code |
| MinimumSpanningTree.matrix | Source code |
| MorphoBankDecode | Man page Source code |
| MrBayesTrees | Man page |
| MultiSplitInformation | Man page Source code |
| N1Spr | Man page Source code |
| NDescendants | Man page Source code |
| NJTree | Man page Source code |
| NPartitionPairs | Man page Source code |
| NPartitions | Man page |
| NRooted | Man page Source code |
| NRooted64 | Man page Source code |
| NRootedShapes | Man page Source code |
| NSplits | Man page Source code |
| NSplits.ClusterTable | Man page Source code |
| NSplits.NULL | Man page Source code |
| NSplits.Splits | Man page Source code |
| NSplits.character | Man page Source code |
| NSplits.list | Man page Source code |
| NSplits.multiPhylo | Man page |
| NSplits.numeric | Man page Source code |
| NSplits.phylo | Man page Source code |
| NTip | Man page Source code |
| NTip.Splits | Man page |
| NTip.default | Man page Source code |
| NTip.list | Man page Source code |
| NTip.matrix | Man page Source code |
| NTip.multiPhylo | Man page Source code |
| NTip.phyDat | Man page Source code |
| NTip.phylo | Man page Source code |
| NUnrooted | Man page Source code |
| NUnrooted64 | Man page Source code |
| NUnrootedMult | Man page Source code |
| NUnrootedShapes | Man page Source code |
| NUnrootedSplits | Man page Source code |
| NewickTree | Man page Source code |
| Neworder | Man page |
| NeworderPhylo | Man page Source code |
| NeworderPruningwise | Man page Source code |
| NexusTokens | Man page Source code |
| NodeDepth | Man page Source code |
| NodeDepth.list | Source code |
| NodeDepth.matrix | Source code |
| NodeDepth.phylo | Source code |
| NodeNumbers | Man page Source code |
| NodeOrder | Man page Source code |
| NodeOrder.list | Source code |
| NodeOrder.matrix | Source code |
| NodeOrder.phylo | Source code |
| PairwiseDistances | Man page Source code |
| PathLengths | Man page Source code |
| PectinateTree | Man page Source code |
| PhyDat | Man page Source code |
| PhyDatToMatrix | Man page Source code |
| PhyDatToString | Man page |
| PhyToString | Man page Source code |
| PhydatToString | Man page |
| PhylogeneticInfo | Man page Source code |
| PhylogeneticInformation | Man page |
| PolarizeSplits | Man page Source code |
| Postorder | Man page Source code |
| Postorder.NULL | Man page Source code |
| Postorder.list | Man page Source code |
| Postorder.multiPhylo | Man page Source code |
| Postorder.numeric | Man page Source code |
| Postorder.phylo | Man page Source code |
| PostorderOrder | Man page Source code |
| PostorderOrder.numeric | Man page Source code |
| PostorderOrder.phylo | Man page Source code |
| Preorder | Man page Source code |
| Preorder.NULL | Man page Source code |
| Preorder.list | Man page Source code |
| Preorder.multiPhylo | Man page Source code |
| Preorder.numeric | Man page Source code |
| Preorder.phylo | Man page Source code |
| Pruningwise | Man page Source code |
| Pruningwise.NULL | Man page Source code |
| Pruningwise.list | Man page Source code |
| Pruningwise.multiPhylo | Man page Source code |
| Pruningwise.phylo | Man page Source code |
| RandomTree | Man page Source code |
| ReadAsPhyDat | Man page Source code |
| ReadCharacters | Man page Source code |
| ReadMrBayes | Man page |
| ReadMrBayesTrees | Man page Source code |
| ReadNotes | Man page Source code |
| ReadTntAsPhyDat | Man page Source code |
| ReadTntCharacters | Man page Source code |
| ReadTntTree | Man page Source code |
| Renumber | Man page Source code |
| RenumberEdges | Man page Source code |
| RenumberTips | Man page Source code |
| RenumberTips.NULL | Man page Source code |
| RenumberTips.list | Man page Source code |
| RenumberTips.multiPhylo | Man page Source code |
| RenumberTips.phylo | Man page Source code |
| RenumberTree | Man page Source code |
| Reorder | Man page |
| RightmostCharacter | Man page Source code |
| RoguePlot | Man page Source code |
| RootNode | Man page Source code |
| RootNode.list | Source code |
| RootNode.numeric | Source code |
| RootNode.phylo | Source code |
| RootNodeDist | Man page |
| RootNodeDistance | Man page Source code |
| RootNodeDistance.character | Man page Source code |
| RootNodeDistance.numeric | Man page Source code |
| RootOnNode | Man page Source code |
| RootOnNode.NULL | Source code |
| RootOnNode.list | Source code |
| RootOnNode.multiPhylo | Source code |
| RootOnNode.phylo | Source code |
| RootTree | Man page Source code |
| RootTree.NULL | Source code |
| RootTree.list | Source code |
| RootTree.matrix | Source code |
| RootTree.multiPhylo | Source code |
| RootTree.phylo | Source code |
| RootedTreeShape | Man page Source code |
| RootedTreeWithShape | Man page Source code |
| RootedTreeWithShape.integer64 | Source code |
| RootedTreeWithShape.numeric | Source code |
| SampleOne | Man page Source code |
| SingleTaxonTree | Man page Source code |
| SisterSize | Man page Source code |
| SisterSize.character | Man page Source code |
| SisterSize.numeric | Man page Source code |
| SortTree | Man page Source code |
| SortTree.list | Man page Source code |
| SortTree.multiPhylo | Man page Source code |
| SortTree.phylo | Man page Source code |
| SpectrumLegend | Man page Source code |
| SplitFrequency | Man page Source code |
| SplitImbalance | Man page Source code |
| SplitImbalance.Splits | Man page Source code |
| SplitImbalance.phylo | Man page |
| SplitInformation | Man page Source code |
| SplitMatchProbability | Man page Source code |
| SplitNumber | Man page Source code |
| Splits | Man page |
| SplitsInBinaryTree | Man page Source code |
| SplitsInBinaryTree.NULL | Man page Source code |
| SplitsInBinaryTree.Splits | Man page |
| SplitsInBinaryTree.default | Man page Source code |
| SplitsInBinaryTree.list | Man page Source code |
| SplitsInBinaryTree.multiPhylo | Man page |
| SplitsInBinaryTree.numeric | Man page Source code |
| SplitsInBinaryTree.phylo | Man page |
| StarTree | Man page Source code |
| Stemwardness | Man page |
| StringToPhyDat | Man page Source code |
| StringToPhydat | Man page |
| Subsplit | Man page Source code |
| Subtree | Man page Source code |
| SupportColor | Man page |
| SupportColour | Man page Source code |
| TCIContext | Man page Source code |
| TCIContext.numeric | Man page Source code |
| TCIContext.phylo | Source code |
| TNTOrder | Man page |
| TNTText2Tree | Man page |
| TipLabels | Man page Source code |
| TipLabels.MixedBase | Man page |
| TipLabels.Splits | Man page |
| TipLabels.TreeNumber | Man page |
| TipLabels.character | Man page Source code |
| TipLabels.default | Man page Source code |
| TipLabels.list | Man page Source code |
| TipLabels.logical | Man page Source code |
| TipLabels.matrix | Man page Source code |
| TipLabels.multiPhylo | Man page Source code |
| TipLabels.numeric | Man page Source code |
| TipLabels.phyDat | Man page Source code Source code |
| TipLabels.phylo | Man page Source code |
| TipTimedTree | Man page Source code |
| TipsInSplits | Man page Source code |
| TipsInSplits.Splits | Man page Source code |
| TipsInSplits.phylo | Man page Source code |
| TntOrder | Man page Source code |
| TntOrder.NULL | Man page Source code |
| TntOrder.list | Man page Source code |
| TntOrder.multiPhylo | Man page Source code |
| TntOrder.numeric | Man page Source code |
| TntOrder.phylo | Man page Source code |
| TntText2Tree | Man page Source code |
| TopologyOnly | Man page Source code |
| TopologyOnly.default | Source code |
| TopologyOnly.list | Source code |
| TopologyOnly.multiPhylo | Source code |
| TopologyOnly.phylo | Source code |
| TotalCopheneticIndex | Man page Source code |
| TotalCopheneticIndex.list | Source code |
| TotalCopheneticIndex.phylo | Source code |
| TreeIsRooted | Man page Source code |
| TreeNumber | Man page |
| TreeShape | Man page |
| TreeSplits | Man page Source code |
| TreeTools | Man page |
| TreeTools-package | Man page |
| TreesMatchingSplit | Man page Source code |
| TreesMatchingTree | Man page Source code |
| TrivialSplits | Man page Source code |
| TrivialTree | Man page |
| Unquote | Man page Source code |
| UnrootTree | Man page Source code |
| UnrootTree.NULL | Source code |
| UnrootTree.list | Source code |
| UnrootTree.multiPhylo | Source code |
| UnrootTree.phylo | Source code |
| UnrootedKeys | Man page |
| UnrootedTreeKey | Man page Source code |
| UnrootedTreeShape | Man page Source code |
| UnrootedTreeWithKey | Man page Source code |
| UnrootedTreeWithShape | Man page Source code |
| UnrootedTreesMatchingSplit | Man page Source code |
| UnshiftTree | Man page Source code |
| WithoutTrivialSplits | Man page Source code |
| WriteTntCharacters | Man page Source code |
| WriteTntCharacters.matrix | Man page Source code |
| WriteTntCharacters.phyDat | Man page Source code |
| YuleTree | Man page Source code |
| ZeroTaxonTree | Man page Source code |
| `!.Splits` | Source code |
| `&.Splits` | Source code |
| `+.Splits` | Source code |
| `-.Splits` | Source code |
| `<.MixedBase` | Source code |
| `<.phylo` | Source code |
| `==.MixedBase` | Source code |
| `==.phylo` | Source code |
| `>.MixedBase` | Source code |
| `>.phylo` | Source code |
| `[[.Splits` | Source code |
| `|.Splits` | Source code |
| and_splits | Source code |
| ape_neworder_phylo | Source code |
| ape_neworder_pruningwise | Source code |
| as.ClusterTable | Man page Source code |
| as.ClusterTable.list | Man page Source code |
| as.ClusterTable.multiPhylo | Man page |
| as.ClusterTable.phylo | Man page Source code |
| as.MixedBase | Man page Source code |
| as.MixedBase.MixedBase | Man page Source code |
| as.MixedBase.TreeNumber | Man page Source code |
| as.MixedBase.integer64 | Man page Source code |
| as.MixedBase.multiPhylo | Man page Source code |
| as.MixedBase.numeric | Man page Source code |
| as.MixedBase.phylo | Man page Source code |
| as.Newick | Man page Source code |
| as.Newick.list | Man page Source code |
| as.Newick.multiPhylo | Man page |
| as.Newick.phylo | Man page Source code |
| as.Splits | Man page Source code |
| as.Splits.Splits | Man page Source code |
| as.Splits.character | Man page Source code |
| as.Splits.list | Man page Source code |
| as.Splits.logical | Man page Source code |
| as.Splits.matrix | Man page Source code |
| as.Splits.multiPhylo | Man page Source code |
| as.Splits.phylo | Man page Source code |
| as.TreeNumber | Man page Source code |
| as.TreeNumber.MixedBase | Man page Source code |
| as.TreeNumber.TreeNumber | Man page Source code |
| as.TreeNumber.character | Man page Source code |
| as.TreeNumber.multiPhylo | Man page Source code |
| as.TreeNumber.phylo | Man page Source code |
| as.character.Splits | Source code |
| as.integer64.TreeNumber | Source code |
| as.logical.Splits | Man page Source code |
| as.logical.phylo | Source code |
| as.matrix.ClusterTable | Man page Source code |
| as.matrix.phyDat | Source code |
| as.matrix.phylo | Source code |
| as.multiPhylo | Man page Source code |
| as.multiPhylo.Splits | Man page Source code |
| as.multiPhylo.list | Man page Source code |
| as.multiPhylo.phyDat | Man page Source code |
| as.multiPhylo.phylo | Man page Source code |
| as.phylo.MixedBase | Man page Source code |
| as.phylo.Splits | Source code |
| as.phylo.TreeNumber | Man page Source code |
| as.phylo.integer64 | Source code |
| as.phylo.numeric | Man page Source code |
| as_newick | Source code |
| brewer | Man page |
| c.Splits | Source code |
| consensus_tree | Source code |
| cpp_edge_to_splits | Source code |
| descendant_edges | Source code |
| descendant_tips | Source code |
| doubleFactorials | Man page |
| duplicated.Splits | Source code |
| duplicated_splits | Source code |
| edge_to_mixed_base | Source code |
| edge_to_num | Source code |
| edge_to_rooted_shape | Source code |
| edge_to_splits | Man page Source code |
| head.Splits | Source code |
| in.Splits | Man page Source code |
| is.TreeNumber | Man page Source code |
| keep_tip | Source code |
| kept_vertices | Source code |
| length.Splits | Source code |
| logDoubleFactorials | Man page |
| mask_splits | Source code |
| match | Man page |
| match,Splits,Splits-method | Man page |
| match.Splits | Man page |
| minimum_spanning_tree | Source code |
| mixed_base_to_parent | Source code |
| nRootedShapes | Man page |
| nUnrootedShapes | Man page |
| names.Splits | Source code |
| not_splits | Source code |
| num_to_parent | Source code |
| or_splits | Source code |
| path_lengths | Source code |
| postorder_order | Source code |
| print.ClusterTable | Man page Source code |
| print.Splits | Source code |
| print.TreeNumber | Man page Source code |
| random_parent | Source code |
| release_questions | Source code |
| replicate64 | Man page Source code |
| rev.Splits | Source code |
| root_binary | Source code |
| root_on_node | Man page Source code |
| rooted_shape_to_edge | Source code |
| sapply64 | Man page Source code |
| sort.multiPhylo | Man page Source code |
| splits_to_edge | Source code |
| summary.ClusterTable | Man page Source code |
| summary.Splits | Source code |
| t.Splits | Source code |
| tail.Splits | Source code |
| thin_splits | Source code |
| tips_in_splits | Source code |
| unique.Splits | Source code |
| unrootedKeys | Man page |
| vapply64 | Man page Source code |
| xor | Man page |
| xor,Splits,Splits-method | Man page |
| xor_splits | Source code |
