Global Comparison of two Phylogenies
Coalescent Intervals
Conversion Among DNA Sequence Internal Formats
Calculate Numbers of Phylogenetic Trees
Compact Display of a Phylogeny
Matrix Exponential
Gene Tree of 36 Landplant rbcL Sequences
Molecular Dating With Mean Path Lengths
Phylogenetic Tree of 193 HIV-1 Sequences
Test if a Tree is Ultrametric
Find Most Recent Common Ancestors Between Pairs
Drawing Skyline Plot Graphs
Axis on Side of Phylogeny
Roots Phylogenetic Trees
Print Summary of a Phylogeny
Internal Ape Functions
Phylogeny of the Orders of Birds From Sibley and Ahlquist
Identifies Edges of a Tree
Collapsed Coalescent Intervals
Internal Reordering of Trees
Define Similarity Matrix
Defines Models of DNA Evolution
Binds Trees
Molecular Dating With Penalized Likelihood
Cheverud's Comparative Method
Blomberg et al.'s Correlation Structure
Topological Distances Between Two Trees
Balance of a Dichotomous Phylogenetic Tree
Population Parameter THETA using Expected Number of Alleles
Conversion Among Tree Objects
Ancestral Character Simulation
Labelling the Nodes, Tips, and Edges of a Tree
Ratogram Computed by Nonparametric Rate Smoothing
Phylogenetic Correlation Structures
Pagel's ``lambda'' Correlation Structure
Collapse and Resolve Multichotomies
Pairwise Distances from a Phylogenetic Tree
Add a Scale Bar to a Phylogeny Plot
Read Character Data In NEXUS Format
Objective Function Employed in Nonparametric Rate Smoothing
Tree Estimation Based on the Minimum Evolution Algorithm
Zoom on a Portion of a Phylogeny by Successive Clicks
Estimating Phylogenies by Maximum Likelihood
Grafen's (1989) Correlation Structure
Population Parameter THETA using Homozygosity
All subtrees of a Phylogenetic Tree
Skyline Plot Estimate of Effective Population Size
Gene Tree of 32 opsin Sequences
Zoom on a Portion of a Phylogeny
Phylogenetic Variance-covariance or Correlation Matrix
Number of Cherries and Null Models of Trees
Read DNA Sequences in a File
Content in GC from DNA Sequences
Lynch's Comparative Method
Ladderize a Tree
Label Management
Ancestral Character Estimation
Plots two phylogenetic trees face to face with links between the tips.
Phylogeny of the Families of Birds From Sibley and Ahlquist
Find Segregating Sites in DNA Sequences
Brownian Correlation Structure
Lineages Through Time Plot
Nucleotide Diversity
Read DNA Sequences from GenBank via Internet
Tests of Constant Diversification Rates
Shimodaira-Hasegawa Test
Comparative Analysis with GEEs
Read Tree File in Nexus Format
Phylogenetically Independent Contrasts
Swopping sister clades
Pairwise Distances from Genetic Data
Analysis of Diversification with Survival Models
Heterozygosity at a Locus Using Gene Frequencies
Test for Binary Tree
Martins's (1997) Correlation Structure
Fits Yule Model to a Phylogenetic Tree
Analyses of Phylogenetics and Evolution
Remove Tips in a Phylogenetic Tree
Klastorin's (1982) method for classifying genes as suggested by Misawa
and Tajima (2000)
Population Parameter THETA using Segregating Sites
in DNA Sequences
Plot Ancestral Character Values on a Tree
Depth of Nodes and Tips
Plot Phylogenies
Base frequencies from DNA Sequences
Fits a Bunch of Models with PhyML
Manipulate DNA Sequences in Bit-Level Format
Conversion Between Phylo and Matching Objects
Generates Random Trees
Write Character Data In NEXUS Format
Chronogram Computed by Nonparametric Rate Smoothing
Read Tree File in CAIC Format
Reversible Jump MCMC to Infer Demographic History
Write DNA Sequences in a File
Conversion from Taxonomy Variables to Phylogenetic Trees
Plot Variance Components
Cytochrome b Gene Sequences of Woodmice
Write Tree File in Nexus Format
Moran's I Autocorrelation Index
Extended Version of the Birth-Death Models to Estimate Speciation
and Extinction Rates
Bat Phylogeny
Graphical Identification of Nodes and Tips
Tree Estimation Based on an Improved Version of the NJ Algorithm
Tree Bipartition and Bootstrapping Phylogenies
Collapse Single Nodes
Mantel Test for Similarity of Two Matrices
Estimation of Speciation and Extinction Rates With Birth-Death Models
Pairwise Distances from DNA Sequences
Ornstein--Uhlenbeck Model for Continuous Characters
Phylogenetic Correlogram
Branch Lengths Computation
Compute Variance Component Estimates
Concensus Trees
Minimum Spanning Tree
NEXUS Data Example
Delete Alignment Gaps in DNA Sequences
Write Tree File in Parenthetic Format
Revomes Duplicate Trees
Fits the Yule Model With Covariates
Neighbor-Joining Tree Estimation
Molecular Phylogeny of Living Xenarthrans
Plot a Correlogram
Initialize a 'corPhyl' Structure Object
Branching Times of a Phylogenetic Tree
Carnivora body sizes and life history traits
Read Tree File in Parenthetic Format
Gamma-Statistic of Pybus and Harvey