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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:

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

Introduced in R2006b

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