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