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