add.scale.bar Add a Scale Bar to a Phylogeny Plot all.equal.phylo Global Comparison of two Phylogenies 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 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 gamma.stat Gamma-Statistic of Pybus and Harvey GC.content Content in GC from DNA Sequences 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 ltt.plot Lineages Through Time Plot mantel.test Mantel Test for Similarity of Two Matrices mst Minimum Spanning Tree NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing opsin Gene Tree of 32 opsin Sequences pic Phylogenetically Independent Contrasts plot.phylo Plot Phylogenies 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 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 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