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