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