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