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