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