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