phylobase

MRCA

Adding data to a phylo4 or a phylo4d object

Tree traversal and utility functions

Validity checking for phylo4 objects

edgeLength methods

Edges accessors

Get tree from tree+data object

Format data for use in phylo4d objects

Data from Darwin's finches

Node and Edge look-up functions

Labels for phylo4/phylo4d objects

multiPhylo4 and extended classes

nTips, nNodes, nEdges

nodeId methods

'Owls' data from ape

Constructor for pdata (phylogenetic data) class

Class "pdata"

The phylo4 class

Create a phylogenetic tree

Tests for presence of data associated with trees stored as phylo4d objects

phylo4d class

Combine a phylogenetic tree with data

Calculate node x and y coordinates

Utilities and Tools for Phylogenetics

Set or return options of phylobase

Bubble plots for phylo4d objects

matrix classes for phylobase

Plot a phylo4 object

print a phylogeny

Create a phylo4, phylo4d or data.frame object from a NEXUS or a Newick file

reordering trees within phylobase objects

Methods to test, access (and modify) the root of a phylo4 object.

Converting between phylo4/phylo4d and other phylogenetic tree formats

shortestPath-methods

Methods for creating subsets of phylogenies

Summary for phylo4/phylo4d objects

Retrieving or updating tip and node data in phylo4d objects

Plotting trees and associated data

Phylogeny plotting

Test trees for polytomies, inline nodes (singletons), or reticulation