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