Analyses of Phylogenetics and Evolution
Amino Acid Sequences
Ancestral Character Estimation
Add a Scale Bar to a Phylogeny Plot
Incomplete Distance Matrix Filling
Alignment Explorer With Multiple Devices
Compare DNA Sets
Global Comparison of two Phylogenies
Print DNA or AA Sequence Alignement
Internal Ape Functions
Analyses of Phylogenetics and Evolution
Tools to Explore Files
Conversion Among DNA Sequence Internal Formats
Split Frequencies and Conversion Among Split Classes
Conversion Between Phylo and Matching Objects
Conversion from Taxonomy Variables to Phylogenetic Trees
Conversion Among Tree and Network Objects
Axis on Side of Phylogeny
Balance of a Dichotomous Phylogenetic Tree
Base frequencies from DNA Sequences
Extended Version of the Birth-Death Models to Estimate Speciation and ...
Time-Dependent Birth-Death Models
Phylogenetic Generalized Linear Mixed Model for Binary Data
Binds Trees
Tree Estimation Based on an Improved Version of the NJ Algorithm
Estimation of Speciation and Extinction Rates With Birth-Death Models
Tree Bipartition and Bootstrapping Phylogenies
Branching Times of a Phylogenetic Tree
Building Lists of Trees
Congruence among distance matrices
Carnivora body sizes and life history traits
Check DNA Alignments
Checking Labels
Check the Structure of a "phylo" Object
Number of Cherries and Null Models of Trees
Molecular Dating With Mean Path Lengths
Molecular Dating With Penalized Likelihood
Molecular Dating by Penalised Likelihood and Maximum Likelihood
Multiple Sequence Alignment with External Applications
Coalescent Intervals
Collapse Single Nodes
Collapsed Coalescent Intervals
Cheverud's Comparative Method
Comparative Analysis with GEEs
Lynch's Comparative Method
Ornstein--Uhlenbeck Model for Continuous Characters
Compare Two "phylo" Objects
Branch Lengths Computation
Compute and Set Branching Times
Concensus Trees
Pairwise Distances from a Phylogenetic Tree
Plots two phylogenetic trees face to face with links between the tips.
Blomberg et al.'s Correlation Structure
Brownian Correlation Structure
Phylogenetic Correlation Structures
Grafen's (1989) Correlation Structure
Martins's (1997) Correlation Structure
Pagel's ``lambda'' Correlation Structure
Correlations among Multiple Traits with Phylogenetic Signal
Phylogenetic Correlogram
Probability Density Under Birth--Death Models
Definition of Vectors for Plotting or Annotating
Vertex Degrees in Trees and Networks
Delete Alignment Gaps in DNA or AA Sequences
Delta Plots
Pairwise Distances from DNA Sequences
Pairwise Distances from Genetic Data
Topological Distances Between Two Trees
Tests of Constant Diversification Rates
Analysis of Diversification with Survival Models
Diversity Contrast Test
Manipulate DNA Sequences in Bit-Level Format
Recode Blocks of Indels
dN/dS Ratio
Remove Tips in a Phylogenetic Tree
Draw Additional Edges on a Plotted Tree
Evolutionary Networks
Incomplete distances and edge weights of unrooted topology
Tree Estimation Based on the Minimum Evolution Algorithm
Gamma-Statistic of Pybus and Harvey
Read Annotations from GenBank
Phylogenetic Tree of 193 HIV-1 Sequences
Calculate Numbers of Phylogenetic Trees
Graphical Identification of Nodes and Tips
Plot of DNA Sequence Alignement
Initialize a `corPhyl' Structure Object
Test for Binary Tree
Check Compatibility of Splits
Is Group Monophyletic
Test if a Tree is Ultrametric
Plot Multiple Chronograms on the Same Scale
Label Management
Ladderize a Tree
Leading and Trailing Alignment Gaps to N
Multiple regression through the origin
Lineages Through Time Plot
Theoretical Lineage-Through Time Plots
Label Management
Makes Node Labels
Mantel Test for Similarity of Two Matrices
Matrix Exponential
McConway-Sims Test of Homogeneous Diversification
Reversible Jump MCMC to Infer Demographic History
Mixed Font Labels for Plotting
Moran's I Autocorrelation Index
Most Parsimonious Reconstruction
Find Most Recent Common Ancestors Between Pairs
Minimum Spanning Tree
Collapse and Resolve Multichotomies
Manipulating Lists of Trees
Minimum Variance Reduction
Neighbor-Joining Tree Estimation
Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
node.dating
Depth and Heights of Nodes and Tips
Labelling the Nodes, Tips, and Edges of a Tree
Find Paths of Nodes
Test of host-parasite coevolution
Principal Coordinate Analysis
Tree Annotation
Fits a Bunch of Models with PhyML
Phylogenetically Independent Orthonormal Contrasts
Phylogenetically Independent Contrasts
Plot a Correlogram
Plot Phylogenies
Extra Fuctions to Plot and Annotate Phylogenies
Plot Variance Components
Plot Tree With Time Axis
Compact Display of a Phylogeny
Random DNA Sequences
Read Tree File in CAIC Format
Read DNA Sequences in a File
Read DNA Sequences from GenBank via Internet
Read GFF Files
Read Character Data In NEXUS Format
Read Tree File in Nexus Format
Read Tree File in Parenthetic Format
Continuous Ancestral Character Estimation
Internal Reordering of Trees
Test of Diversification-Shift With the Yule Process
Tree Simulation Under the Time-Dependent Birth--Death Models
Roots Phylogenetic Trees
Swapping Sister Clades
Continuous Character Simulation
Discrete Character Simulation
Multivariate Character Simulation
Generate Random Trees
Root a Tree by Root-to-Tip Regression
Construction of Consensus Distance Matrix With SDM
Find Segregating Sites in DNA Sequences
Skyline Plot Estimate of Effective Population Size
Drawing Skyline Plot Graphs
Slowinski-Guyer Test of Homogeneous Diversification
Solve Ambiguous Bases in DNA Sequences
Species Tree Estimation
Generates Systematic Regular Trees
Zoom on a Portion of a Phylogeny by Successive Clicks
All subtrees of a Phylogenetic Tree
Print Summary of a Phylogeny
Translation from DNA to Amino Acid Sequences
Tree Popping
Tree Explorer With Multiple Devices
Tree Reconstruction Based on the Triangles Method
Revomes Duplicate Trees
Update Labels
Compute Variance Component Estimates
Variance Components with Orthonormal Contrasts
Phylogenetic Variance-covariance or Correlation Matrix
Variance-Covariance Matrix to Tree
Define Similarity Matrix
Find Patterns in DNA Sequences
Identifies Edges of a Tree
Write DNA Sequences in a File
Write Character Data in NEXUS Format
Write Tree File in Nexus Format
Write Tree File in Parenthetic Format
Fits the Yule Model With Covariates
Fits the Yule Model to a Phylogenetic Tree
Fits the Time-Dependent Yule Model
Zoom on a Portion of a Phylogeny
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.