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