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