phytree object

Data structure containing phylogenetic tree

Description

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:

cluster	Validate clusters in phylogenetic tree
get	Retrieve information about phylogenetic tree object
getbyname	Branches and leaves from phytree object
getcanonical	Calculate canonical form of phylogenetic tree
getmatrix	Convert phytree object into relationship matrix
getnewickstr	Create Newick-formatted character vector
pdist	Calculate pairwise patristic distances in phytree object
plot	Draw phylogenetic tree
prune	Remove branch nodes from phylogenetic tree
reorder	Reorder leaves of phylogenetic tree
reroot	Change root of phylogenetic tree
select	Select tree branches and leaves in phytree object
subtree	Extract phylogenetic subtree
view	View phylogenetic tree
weights	Calculate weights for phylogenetic tree

Property Summary

Note

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

Property	Description
NumLeaves	Number of leaves
NumBranches	Number of branches
NumNodes	Number of nodes (NumLeaves + NumBranches)
Pointers	Branch to leaf/branch connectivity list
Distances	Edge length for every leaf/branch
LeafNames	Names of the leaves
BranchNames	Names of the branches
NodeNames	Names of all the nodes

Version History

Introduced in R2006b