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