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