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