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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 (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 string
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

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

See Also

Bioinformatics Toolbox functions: phytree (object constructor), phytreeread, phytreetool, phytreewrite, seqlinkage, seqneighjoin, seqpdist

Bioinformatics Toolbox methods of phytree object: cluster, get, getbyname, getcanonical, getmatrix, getnewickstr, pdist, plot, prune, reroot, select, subtree, view, weights

pfamhmmread

phytree

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