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