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