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