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