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