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