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