CADM.global Congruence among distance matrices DNAbin Manipulate DNA Sequences in Bit-Level Format FastME Tree Estimation Based on the Minimum Evolution Algorithm Initialize.corPhyl Initialize a 'corPhyl' Structure Object LTT Theoretical Lineage-Through Time Plots MPR Most Parsimonious Reconstruction Moran.I Moran's I Autocorrelation Index SDM Construction of Consensus Distance Matrix With SDM ace Ancestral Character Estimation add.scale.bar Add a Scale Bar to a Phylogeny Plot additive Incomplete Distance Matrix Filling alex Alignment Explorer With Multiple Devices all.equal.phylo Global Comparison of two Phylogenies ape-package Analyses of Phylogenetics and Evolution as.alignment Conversion Among DNA Sequence Internal Formats as.bitsplits Split Frequencies and Conversion Among Split Classes as.matching Conversion Between Phylo and Matching Objects as.phylo Conversion Among Tree and Network Objects as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees 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 bd.time Time-Dependent Birth-Death Models bind.tree Binds Trees bionj Tree Estimation Based on an Improved Version of the NJ Algorithm 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 c.phylo Building Lists of Trees carnivora Carnivora body sizes and life history traits cherry Number of Cherries and Null Models of Trees chiroptera Bat Phylogeny chronoMPL Molecular Dating With Mean Path Lengths chronopl Molecular Dating With Penalized Likelihood chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood clustal Multiple Sequence Alignment with External Applications coalescent.intervals Coalescent Intervals 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 compute.brtime Compute and Set Branching Times consensus Concensus Trees cophenetic.phylo Pairwise Distances from a Phylogenetic Tree cophyloplot Plots two phylogenetic trees face to face with links between the tips. corBlomberg Blomberg et al.'s Correlation Structure corBrownian Brownian Correlation Structure corClasses Phylogenetic Correlation Structures corGrafen Grafen's (1989) Correlation Structure corMartins Martins's (1997) Correlation Structure corPagel Pagel's "lambda" Correlation Structure correlogram.formula Phylogenetic Correlogram data.nex NEXUS Data Example dbd Probability Density Under Birth-Death Models del.gaps Delete Alignment Gaps in DNA Sequences delta.plot Delta Plots dist.dna Pairwise Distances from DNA Sequences dist.gene Pairwise Distances from Genetic Data dist.topo Topological Distances Between Two Trees diversi.gof Tests of Constant Diversification Rates diversi.time Analysis of Diversification with Survival Models diversity.contrast.test Diversity Contrast Test drop.tip Remove Tips in a Phylogenetic Tree edges Draw Additional Edges on a Plotted Tree evonet Evolutionary Networks ewLasso Incomplete distances and edge weights of unrooted topology gammaStat Gamma-Statistic of Pybus and Harvey hivtree Phylogenetic Tree of 193 HIV-1 Sequences howmanytrees Calculate Numbers of Phylogenetic Trees identify.phylo Graphical Identification of Nodes and Tips image.DNAbin Plot of DNA Sequence Alignement is.binary.tree Test for Binary Tree is.compatible Check Compatibility of Splits is.monophyletic Is Group Monophyletic is.ultrametric Test if a Tree is Ultrametric kronoviz Plot Multiple Chronograms on the Same Scale ladderize Ladderize a Tree landplants Gene Tree of 36 Landplant rbcL Sequences lmorigin Multiple regression through the origin ltt.plot Lineages Through Time Plot makeLabel Label Management makeNodeLabel Makes Node Labels mantel.test Mantel Test for Similarity of Two Matrices mat3 Three Matrices mat5M3ID Five Trees mat5Mrand Five Independent Trees matexpo Matrix Exponential mcconwaysims.test McConway-Sims Test of Homogeneous Diversification mcmc.popsize Reversible Jump MCMC to Infer Demographic History mixedFontLabel Mixed Font Labels for Plotting mrca Find Most Recent Common Ancestors Between Pairs mst Minimum Spanning Tree multi2di Collapse and Resolve Multichotomies multiphylo Manipulating Lists of Trees mvr Minimum Variance Reduction nj Neighbor-Joining Tree Estimation njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* node.depth Depth and Heights of Nodes and Tips nodelabels Labelling the Nodes, Tips, and Edges of a Tree opsin Gene Tree of 32 opsin Sequences parafit Test of host-parasite coevolution pcoa Principal Coordinate Analysis phydataplot Tree Annotation phymltest Fits a Bunch of Models with PhyML pic Phylogenetically Independent Contrasts pic.ortho Phylogenetically Independent Orthonormal Contrasts plot.correlogram Plot a Correlogram plot.phylo Plot Phylogenies plot.varcomp Plot Variance Components print.phylo Compact Display of a Phylogeny rTraitCont Continuous Character Simulation rTraitDisc Discrete Character Simulation rTraitMult Multivariate Character Simulation read.GenBank Read DNA Sequences from GenBank via Internet read.caic Read Tree File in CAIC Format read.dna Read DNA Sequences in a File 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 richness.yule.test Test of Diversification-Shift With the Yule Process rlineage Tree Simulation Under the Time-Dependent Birth-Death Models root Roots Phylogenetic Trees rotate Swapping Sister Clades rtree Generates Random Trees rtt Root a Tree by Root-to-Tip Regression seg.sites Find Segregating Sites in DNA Sequences skyline Skyline Plot Estimate of Effective Population Size skylineplot Drawing Skyline Plot Graphs slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification speciesTree Species Tree Estimation stree Generates Systematic Regular Trees subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks subtrees All subtrees of a Phylogenetic Tree summary.phylo Print Summary of a Phylogeny treePop Tree Popping trex Tree Explorer With Multiple Devices triangMtd Tree Reconstruction Based on the Triangles Method unique.multiPhylo Revomes Duplicate Trees varCompPhylip Variance Components with Orthonormal Contrasts varcomp Compute Variance Component Estimates vcv Phylogenetic Variance-covariance or Correlation Matrix weight.taxo Define Similarity Matrix where Find Patterns in DNA Sequences 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 yule Fits the Yule Model to a Phylogenetic Tree yule.cov Fits the Yule Model With Covariates yule.time Fits the Time-Dependent Yule Model zoom Zoom on a Portion of a Phylogeny