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