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