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