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