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