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