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