Man pages for TreeTools
Create, Modify and Analyse Phylogenetic Trees
| AddTip | Add a tip to a phylogenetic tree |
| AncestorEdge | Ancestral edge |
| ApeTime | Read modification time from "ape" Nexus file |
| ArtificialExtinction | Artificial Extinction |
| as.multiPhylo | Convert object to 'multiPhylo' class |
| as.Newick | Write a phylogenetic tree in Newick format |
| brewer | Brewer palettes |
| CharacterInformation | Character information content |
| CladeSizes | Clade sizes |
| CladisticInfo | Cladistic information content of a tree |
| ClusterTable | Convert phylogenetic tree to 'ClusterTable' |
| ClusterTable-methods | S3 methods for 'ClusterTable' objects |
| CollapseNode | Collapse nodes on a phylogenetic tree |
| CompatibleSplits | Which splits are compatible? |
| Consensus | Construct consensus trees |
| ConsensusWithout | Reduced consensus, omitting specified taxa |
| ConstrainedNJ | Constrained neighbour-joining tree |
| DescendantEdges | Identify descendant edges |
| dot-RandomParent | Random parent vector |
| DoubleFactorial | Double factorial |
| doubleFactorials | Double factorials |
| DropTip | Drop leaves from tree |
| EdgeAncestry | Ancestors of an edge |
| EdgeDistances | Distance between edges |
| edge_to_splits | Efficiently convert edge matrix to splits |
| EndSentence | Add full stop to end of a sentence |
| EnforceOutgroup | Generate a tree with a specified outgroup |
| ExtractTaxa | Extract taxa from a matrix block |
| GenerateTree | Generate pectinate, balanced or random trees |
| Hamming | Hamming distance between taxa in a phylogenetic dataset |
| ImposeConstraint | Force a tree to match a constraint |
| is.TreeNumber | Is an object a 'TreeNumber' object? |
| KeptPaths | Paths present in reduced tree |
| KeptVerts | Identify vertices retained when leaves are dropped |
| LabelSplits | Label splits |
| LeafLabelInterchange | Leaf label interchange |
| ListAncestors | List ancestors |
| Lobo.data | Data from Zhang et al. 2016 |
| logDoubleFactorials | Natural logarithms of double factorials |
| MakeTreeBinary | Generate binary tree by collapsing polytomies |
| MatchEdges | Match nodes and edges between trees |
| match.Splits | Split matching |
| MatrixToPhyDat | Convert between matrices and 'phyDat' objects |
| MorphoBankDecode | Decode MorphoBank text |
| MRCA | Most recent common ancestor |
| MSTEdges | Minimum spanning tree |
| N1Spr | Number of trees one SPR step away |
| NDescendants | Count descendants for each node in a tree |
| NewickTree | Write Newick Tree |
| Neworder | Reorder edges of a phylogenetic tree |
| NJTree | Generate a neighbour joining tree |
| NodeDepth | Distance of each node from tree exterior |
| NodeNumbers | Numeric index of each node in a tree 'NodeNumbers()' returns... |
| NodeOrder | Number of edges incident to each node in a tree |
| NPartitionPairs | Distributions of tips consistent with a partition pair |
| NRooted | Number of trees |
| nRootedShapes | Number of rooted / unrooted tree shapes |
| NSplits | Number of distinct splits |
| NTip | Number of leaves in a phylogenetic tree |
| PairwiseDistances | Distances between each pair of trees |
| PathLengths | Calculate length of paths between each pair of vertices... |
| PhyToString | Convert between strings and 'phyDat' objects |
| PolarizeSplits | Polarize splits on a single taxon |
| print.TreeNumber | Print 'TreeNumber' object |
| ReadCharacters | Read phylogenetic characters from file |
| ReadMrBayesTrees | Read posterior tree sample produced by MrBayes |
| ReadTntTree | Parse TNT Tree |
| Renumber | Renumber a tree's nodes and tips |
| RenumberTips | Renumber a tree's tips |
| Reorder | Reorder tree edges and nodes |
| RightmostCharacter | Rightmost character of string |
| RoguePlot | Visualize position of rogue taxa |
| RootNode | Which node is a tree's root? |
| root_on_node | Wrapper for internal C function 'root_on_node()' |
| RootTree | Root or unroot a phylogenetic tree |
| SampleOne | Quickly sample |
| sapply64 | Apply a function that returns 64-bit integers over a list or... |
| sort.multiPhylo | Sort a list of phylogenetic trees |
| SortTree | Sort tree |
| SpectrumLegend | Produce a legend for continuous gradient scales |
| SplitFrequency | Frequency of splits |
| SplitInformation | Phylogenetic information content of splitting leaves into two... |
| SplitMatchProbability | Probability of matching this well |
| Splits | Convert object to 'Splits' |
| SplitsInBinaryTree | Maximum splits in an _n_-leaf tree |
| Stemwardness | "Stemwardness" of a leaf |
| Subsplit | Subset of a split on fewer leaves |
| Subtree | Extract a subtree |
| SupportColour | Colour for node support value |
| TipLabels | Extract tip labels |
| TipsInSplits | Tips contained within splits |
| TipTimedTree | Display time-calibrated tree using tip information only |
| TotalCopheneticIndex | Total Cophenetic Index |
| TreeIsRooted | Is tree rooted? |
| TreeNumber | Unique integer indices for bifurcating tree topologies |
| TreeShape | Integer representing shape of a tree |
| TreesMatchingSplit | Number of trees matching a bipartition split |
| TreesMatchingTree | Number of trees containing a tree |
| TreeTools-package | TreeTools |
| TrivialSplits | Identify and remove trivial splits |
| TrivialTree | Generate trivial trees |
| Unquote | Remove quotation marks from a string |
| UnrootedTreesMatchingSplit | Number of trees consistent with split |
| UnshiftTree | Add tree to start of list |
| WriteTntCharacters | Write morphological character matrix to TNT file |
| xor | Exclusive OR operation |
