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A B C D E F G H I K L M N O P R S T U V W X Y Z misc
| ace | Ancestral Character Estimation |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot |
| AIC.ace | Ancestral Character Estimation |
| AIC.phylo | Estimating Phylogenies by Maximum Likelihood |
| all.equal.phylo | Global Comparison of two Phylogenies |
| anova.ace | Ancestral Character Estimation |
| as.alignment | Conversion Among DNA Sequence Internal Formats |
| as.character.DNAbin | Conversion Among DNA Sequence Internal Formats |
| as.DNAbin | Conversion Among DNA Sequence Internal Formats |
| as.hclust.phylo | Conversion Among Tree Objects |
| as.matching | Conversion Between Phylo and Matching Objects |
| as.phylo | Conversion Among Tree Objects |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees |
| as.phylo.hclust | Conversion Among Tree Objects |
| as.phylo.matching | Conversion Between Phylo and Matching Objects |
| as.phylo.phylog | Conversion Among Tree Objects |
| axisPhylo | Axis on Side of Phylogeny |
| balance | Balance of a Dichotomous Phylogenetic Tree |
| base.freq | Base frequencies from DNA Sequences |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates |
| 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 |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies |
| branching.times | Branching Times of a Phylogenetic Tree |
| carnivora | Carnivora body sizes and life history traits |
| cbind.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
| cherry | Number of Cherries and Null Models of Trees |
| chiroptera | Bat Phylogeny |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing |
| chronopl | Molecular Dating With Penalized Likelihood |
| coalescent.intervals | Coalescent Intervals |
| coef.corBrownian | Brownian Correlation Structure |
| coef.corGrafen | Grafen's (1989) Correlation Structure |
| coef.corMartins | Martins's (1997) Correlation Structure |
| collapse.singles | Collapse Single Nodes |
| collapsed.intervals | Collapsed Coalescent Intervals |
| compar.cheverud | Cheverud's Comparative Method |
| compar.gee | Comparative Analysis with GEEs |
| compar.lynch | Lynch's Comparative Method |
| compar.ou | Ornstein-Uhlenbeck Model for Continuous Characters |
| compute.brlen | Branch Lengths Computation |
| consensus | Concensus Trees |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree |
| corBrownian | Brownian Correlation Structure |
| corClasses | Phylogenetic Correlation Structures |
| corGrafen | Grafen's (1989) Correlation Structure |
| corMartins | Martins's (1997) Correlation Structure |
| corMatrix.corBrownian | Brownian Correlation Structure |
| corMatrix.corGrafen | Grafen's (1989) Correlation Structure |
| corMatrix.corMartins | Martins's (1997) Correlation Structure |
| corPhyl | Phylogenetic Correlation Structures |
| Correlogram | Compute a correlogram |
| correlogram.formula | Compute a correlogram |
| correlogram.phylo | Compute a correlogram |
| cynipids | NEXUS Data Example |
| data.nex | NEXUS Data Example |
| deviance.ace | Ancestral Character Estimation |
| deviance.phylo | Estimating Phylogenies by Maximum Likelihood |
| di2multi | Collapse and Resolve Multichotomies |
| discrete.dist | Taxonomic Level from a Pairwise Distances Matrix |
| dist.dna | Pairwise Distances from DNA Sequences |
| dist.gene | Pairwise Distances from Genetic Data |
| dist.nodes | Pairwise Distances from a Phylogenetic Tree |
| dist.topo | Topological Distances Between Two Trees |
| diversi.gof | Tests of Constant Diversification Rates |
| diversi.time | Analysis of Diversification with Survival Models |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format |
| DNAmodel | Defines Models of DNA Evolution |
| drop.tip | Remove Tips in a Phylogenetic Tree |
| drop1.compar.gee | Comparative Analysis with GEEs |
| edgelabels | Labelling the Nodes, Tips, and Edges of a Tree |
| evolve.phylo | Ancestral Character Simulation |
| extract.popsize | Reversible Jump MCMC to Infer Demographic History |
| 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 |
| howmanytrees | Calculate Numbers of Phylogenetic Trees |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object |
| is.binary.tree | Test for Binary Tree |
| is.rooted | Roots Phylogenetic Trees |
| is.ultrametric | Test if a Tree is Ultrametric |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) |
| ladderize | Ladderize a Tree |
| landplants | Gene Tree of 36 Landplant rbcL Sequences |
| lines.popsize | Reversible Jump MCMC to Infer Demographic History |
| lines.skyline | Drawing Skyline Plot Graphs |
| logLik.ace | Ancestral Character Estimation |
| logLik.phylo | Estimating Phylogenies by Maximum Likelihood |
| ltt.lines | Lineages Through Time Plot |
| ltt.plot | Lineages Through Time Plot |
| mantel.test | Mantel Test for Similarity of Two Matrices |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History |
| mlphylo | Estimating Phylogenies by Maximum Likelihood |
| mltt.plot | Lineages Through Time Plot |
| Moran.I | Moran's I Autocorrelation Index |
| mrca | Find Most Recent Common Ancestors Between Pairs |
| mst | Minimum Spanning Tree |
| multi2di | Collapse and Resolve Multichotomies |
| Nedge | Print Summary of a Phylogeny |
| new2old.phylo | Conversion Among Tree Objects |
| nj | Neighbor-Joining Tree Estimation |
| Nnode | Print Summary of a Phylogeny |
| node.depth | Depth of Nodes and Tips |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing |
| Ntip | Print Summary of a Phylogeny |
| nuc.div | Nucleotide Diversity |
| old2new.phylo | Conversion Among Tree Objects |
| opsin | Gene Tree of 32 opsin Sequences |
| panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. |
| phymltest | Fits a Bunch of Models with PHYML |
| pic | Phylogenetically Independent Contrasts |
| plot.ancestral | Plot Ancestral Character Values on a Tree |
| plot.correlogram | Plot a Correlogram |
| plot.correlogramList | Plot several Correlograms |
| plot.mst | Minimum Spanning Tree |
| plot.multi.tree | Plot Phylogenies |
| plot.phylo | Plot Phylogenies |
| plot.phymltest | Fits a Bunch of Models with PHYML |
| plot.popsize | Reversible Jump MCMC to Infer Demographic History |
| plot.skyline | Drawing Skyline Plot Graphs |
| plot.varcomp | Plot Variance Components |
| print.birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models |
| print.compar.gee | Comparative Analysis with GEEs |
| print.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
| print.multi.tree | Compact Display of a Phylogeny |
| print.phylo | Compact Display of a Phylogeny |
| print.phymltest | Fits a Bunch of Models with PHYML |
| print.prop.part | Tree Bipartition and Bootstrapping Phylogenies |
| prop.clades | Tree Bipartition and Bootstrapping Phylogenies |
| prop.part | Tree Bipartition and Bootstrapping Phylogenies |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing |
| rbind.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
| rcoal | Generates Random Trees |
| read.caic | Read Tree File in CAIC Format |
| 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.nexus.data | Read Character Data In NEXUS Format |
| read.tree | Read Tree File in Parenthetic Format |
| reorder.phylo | Internal Reordering of Trees |
| root | Roots Phylogenetic Trees |
| rtree | Generates Random Trees |
| seg.sites | Find Segregating Sites in DNA Sequences |
| sh.test | Shimodaira-Hasegawa Test |
| skyline | Skyline Plot Estimate of Effective Population Size |
| skylineplot | Drawing Skyline Plot Graphs |
| summary.DNAbin | Manipulate DNA Sequences in Bit-Level Format |
| summary.phylo | Print Summary of a Phylogeny |
| summary.phymltest | Fits a Bunch of Models with PHYML |
| summary.prop.part | Tree Bipartition and Bootstrapping Phylogenies |
| 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 |
| tiplabels | Labelling the Nodes, Tips, and Edges of a Tree |
| unroot | Roots Phylogenetic Trees |
| varcomp | Compute Variance Component Estimates |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix |
| weight.taxo | Pairwise Distances from a Taxonomic Level |
| which.edge | Identifies Edges of a Tree |
| woodmouse | Cytochrome b Gene Sequences of Woodmice |
| write.dna | Write DNA Sequences in a File |
| write.nexus | Write Tree File in Nexus Format |
| write.nexus.data | Write Character Data 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 |
| yule.cov | Fits the Yule Model With Covariates |
| zoom | Zoom on a Portion of a Phylogeny |
| [.DNAbin | Manipulate DNA Sequences in Bit-Level Format |