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