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