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