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