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A B C D F G H I K L M N O P R S T V W X Y Z
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot |
| all.equal.phylo | Global Comparison of two Phylogenies |
| as.hclust.phylo | Conversion between "phylo" and "hclust" trees |
| as.phylo | Conversion between "phylo" and "hclust" trees |
| balance | Balance of a Dichotomous Phylogenetic Tree |
| base.freq | Base frequencies from DNA Sequences |
| bind.tree | Binds Trees |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models |
| branching.times | Branching Times of a Phylogenetic Tree |
| cherry | Number of Cherries and Null Models of Trees |
| chiroptera | Bat Phylogeny |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing |
| coalescent.intervals | Coalescent Intervals |
| collapsed.intervals | Collapsed Coalescent Intervals |
| compar.gee | Comparative Analysis with GEEs |
| compar.lynch | Lynch's Comparative Method |
| dist.dna | Pairwise Distances from DNA Sequences |
| dist.gene | Pairwise Distances from Genetic Data |
| dist.phylo | Pairwise Distances from a Phylogenetic Tree |
| diversi.gof | Tests of Constant Diversification Rates |
| diversi.time | Analysis of Diversification with Survival Models |
| drop.tip | Remove Tips in a Phylogenetic Tree |
| find.skyline.epsilon | Skyline Plot Estimate of Effective Population Size |
| gammaStat | Gamma-Statistic of Pybus and Harvey |
| GC.content | Content in GC from DNA Sequences |
| H | Heterozygosity at a Locus Using Gene Frequencies |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences |
| is.binary.tree | Test for Binary Tree |
| is.ultrametric | Test if a Tree is Ultrametric |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) |
| landplants | Gene Tree of 36 Landplant rbcL Sequences |
| lines.skyline | Drawing Skyline Plot Graphs |
| ltt.lines | Lineages Through Time Plot |
| ltt.plot | Lineages Through Time Plot |
| mantel.test | Mantel Test for Similarity of Two Matrices |
| mltt.plot | Lineages Through Time Plot |
| mst | Minimum Spanning Tree |
| node.depth | Depth of Nodes and Tips |
| node.depth.edgelength | Distance from Root to Nodes and Tips |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing |
| opsin | Gene Tree of 32 opsin Sequences |
| pic | Phylogenetically Independent Contrasts |
| plot.mst | Minimum Spanning Tree |
| plot.phylo | Plot Phylogenies |
| plot.skyline | Drawing Skyline Plot Graphs |
| print.compar.gee | Comparative Analysis with GEEs |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing |
| read.dna | Read DNA Sequences in a File |
| read.GenBank | Read DNA Sequences from GenBank via Internet |
| read.nexus | Read Tree File in Nexus Format |
| read.tree | Read Tree File in Parenthetic Format |
| rtree | Generates Random Trees |
| seg.sites | Find Segregating Sites in DNA Sequences |
| skyline | Skyline Plot Estimate of Effective Population Size |
| skylineplot | Drawing Skyline Plot Graphs |
| summary.phylo | Print Summary of a Phylogeny |
| theta.h | Population Parameter THETA using Homozygosity |
| theta.k | Population Parameter THETA using Expected Number of Alleles |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix |
| woodmouse | Cytochrome b Sequences of Woodmice |
| write.dna | Write DNA Sequences in a File |
| write.nexus | Write Tree File in Nexus Format |
| write.tree | Write Tree File in Parenthetic Format |
| xenarthra | Molecular Phylogeny of Living Xenarthrans |
| yule | Fits Yule Model to a Phylogenetic Tree |
| zoom | Zoom on a Portion of a Phylogeny |