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