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