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