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