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