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