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