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