Conversion Among Tree Objects
Lineages Through Time Plot
Klastorin's (1982) method for classifying genes as suggested by Misawa
and Tajima (2000)
Analysis of Diversification with Survival Models
Estimation of Speciation and Extinction Rates With Birth-Death Models
Number of Cherries and Null Models of Trees
Add a Scale Bar to a Phylogeny Plot
Read Tree File in Nexus Format
Collapse Single Nodes
Tree Bipartition and Bootstrapping Phylogenies
Phylogeny of the Families of Birds From Sibley and Ahlquist
Pairwise Distances from a Phylogenetic Tree
Base frequencies from DNA Sequences
Nucleotide Diversity
Axis on Side of Phylogeny
Phylogenetic Correlation Structures
Mantel Test for Similarity of Two Matrices
Ornstein--Uhlenbeck Model for Continuous Characters
Concensus Trees
Balance of a Dichotomous Phylogenetic Tree
Objective Function Employed in Nonparametric Rate Smoothing
NEXUS Data Example
Molecular Dating With Penalized Likelihood
Minimum Spanning Tree
Branching Times of a Phylogenetic Tree
Tests of Constant Diversification Rates
Plot Ancestral Character Values on a Tree
Conversion Between Phylo and Matching Objects
Ladderize a Tree
Calculate Numbers of Phylogenetic Trees
Defines Models of DNA Evolution
Global Comparison of two Phylogenies
Gamma-Statistic of Pybus and Harvey
Compute a correlogram
Lynch's Comparative Method
Taxonomic Level from a Pairwise Distances Matrix
Heterozygosity at a Locus Using Gene Frequencies
Plot a Correlogram
Test if a Tree is Ultrametric
Compact Display of a Phylogeny
Remove Tips in a Phylogenetic Tree
Read DNA Sequences from GenBank via Internet
Roots Phylogenetic Trees
Neighbor-Joining Tree Estimation
Population Parameter THETA using Segregating Sites
in DNA Sequences
Read DNA Sequences in a File
Shimodaira-Hasegawa Test
Pairwise Distances from a Taxonomic Level
Labelling the Nodes, Tips, and Edges of a Tree
Cheverud's Comparative Method
Collapsed Coalescent Intervals
Chronogram Computed by Nonparametric Rate Smoothing
Find Segregating Sites in DNA Sequences
Print Summary of a Phylogeny
Population Parameter THETA using Homozygosity
Fits Yule Model to a Phylogenetic Tree
Population Parameter THETA using Expected Number of Alleles
Internal Reordering of Trees
Ratogram Computed by Nonparametric Rate Smoothing
Depth of Nodes and Tips
Moran's I Autocorrelation Index
Branch Lengths Computation
Initialize a 'corPhyl' Structure Object
Compute Variance Component Estimates
Pairwise Distances from Genetic Data
Write Tree File in Nexus Format
Pairwise Distances from DNA Sequences
Fits a Bunch of Models with PHYML
Content in GC from DNA Sequences
Generates Random Trees
Binds Trees
Carnivora body sizes and life history traits
Coalescent Intervals
Collapse and Resolve Multichotomies
Write Character Data In NEXUS Format
Comparative Analysis with GEEs
Phylogeny of the Orders of Birds From Sibley and Ahlquist
Gene Tree of 32 opsin Sequences
Read Tree File in CAIC Format
Cytochrome b Gene Sequences of Woodmice
Estimating Phylogenies by Maximum Likelihood
Write DNA Sequences in a File
Write Tree File in Parenthetic Format
Identifies Edges of a Tree
Molecular Phylogeny of Living Xenarthrans
Ancestral Character Estimation
Bat Phylogeny
Conversion from Taxonomy Variables to Phylogenetic Trees
Brownian Correlation Structure
Phylogenetic Tree of 193 HIV-1 Sequences
Grafen's (1989) Correlation Structure
Reversible Jump MCMC to Infer Demographic History
Phylogenetically Independent Contrasts
Ancestral Character Simulation
Topological Distances Between Two Trees
panel.superpose.correlogram
Lattice panel used in 'plot.correlogramList'.
Internal Ape Functions
Find Most Recent Common Ancestors Between Pairs
Gene Tree of 36 Landplant rbcL Sequences
Plot Phylogenies
Skyline Plot Estimate of Effective Population Size
Fits the Yule Model With Covariates
Extended Version of the Birth-Death Models to Estimate Speciation
and Extinction Rates
Read Tree File in Parenthetic Format
Plot several Correlograms
Read Character Data In NEXUS Format
Phylogenetic Variance-covariance or Correlation Matrix
Zoom on a Portion of a Phylogeny
Drawing Skyline Plot Graphs
Plot Variance Components
Martins's (1997) Correlation Structure
Test for Binary Tree