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phytree object

Data structure containing phylogenetic tree


A phytree object is a data structure containing a phylogenetic tree. Phylogenetic trees are binary rooted trees, which means that each branch is the parent of two other branches, two leaves, or one branch and one leaf. A phytree object can be ultrametric or nonultrametric.

Method Summary

Following are methods of a phytree object:

clusterValidate clusters in phylogenetic tree
getRetrieve information about phylogenetic tree object
getbynameBranches and leaves from phytree object
getcanonicalCalculate canonical form of phylogenetic tree
getmatrixConvert phytree object into relationship matrix
getnewickstrCreate Newick-formatted character vector
pdistCalculate pairwise patristic distances in phytree object
plotDraw phylogenetic tree
pruneRemove branch nodes from phylogenetic tree
reorderReorder leaves of phylogenetic tree
rerootChange root of phylogenetic tree
selectSelect tree branches and leaves in phytree object
subtreeExtract phylogenetic subtree
viewView phylogenetic tree
weightsCalculate weights for phylogenetic tree

Property Summary


You cannot modify these properties directly. You can access these properties using the get method.

NumLeavesNumber of leaves
NumBranchesNumber of branches
NumNodesNumber of nodes (NumLeaves + NumBranches)
PointersBranch to leaf/branch connectivity list
Distances Edge length for every leaf/branch
LeafNamesNames of the leaves
BranchNamesNames of the branches
NodeNamesNames of all the nodes

Version History

Introduced in R2006b