Man pages for ape
Analyses of Phylogenetics and Evolution
| AAbin | Amino Acid Sequences |
| ace | Ancestral Character Estimation |
| additive | Incomplete Distance Matrix Filling |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot |
| alex | Alignment Explorer With Multiple Devices |
| all.equal.DNAbin | Compare DNA Sets |
| all.equal.phylo | Global Comparison of two Phylogenies |
| alview | Print DNA or AA Sequence Alignement |
| ape-internal | Internal Ape Functions |
| ape-package | Analyses of Phylogenetics and Evolution |
| apetools | Tools to Explore Files |
| 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... |
| bd.time | Time-Dependent Birth-Death Models |
| binaryPGLMM | Phylogenetic Generalized Linear Mixed Model for Binary Data |
| bind.tree | Binds Trees |
| bionj | Tree Estimation Based on an Improved Version of the NJ... |
| 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... |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies |
| branching.times | Branching Times of a Phylogenetic Tree |
| CADM.global | Congruence among distance matrices |
| carnivora | Carnivora body sizes and life history traits |
| checkAlignment | Check DNA Alignments |
| checkLabel | Checking Labels |
| checkValidPhylo | Check the Structure of a "phylo" Object |
| 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... |
| clustal | Multiple Sequence Alignment with External Applications |
| coalescent.intervals | Coalescent Intervals |
| collapsed.intervals | Collapsed Coalescent Intervals |
| collapse.singles | Collapse Single Nodes |
| compar.cheverud | Cheverud's Comparative Method |
| comparePhylo | Compare Two "phylo" Objects |
| 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... |
| 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 |
| corphylo | Correlations among Multiple Traits with Phylogenetic Signal |
| correlogram.formula | Phylogenetic Correlogram |
| c.phylo | Building Lists of Trees |
| cynipids | NEXUS Data Example |
| dbd | Probability Density Under Birth-Death Models |
| def | Definition of Vectors for Plotting or Annotating |
| degree | Vertex Degrees in Trees and Networks |
| del.gaps | Delete Alignment Gaps in DNA or AA 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 |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format |
| DNAbin2indel | Recode Blocks of Indels |
| dnds | dN/dS Ratio |
| 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 |
| fastme | Tree Estimation Based on the Minimum Evolution Algorithm |
| gammaStat | Gamma-Statistic of Pybus and Harvey |
| getAnnotationsGenBank | Read Annotations from GenBank |
| 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 |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object |
| 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 |
| label2table | Label Management |
| ladderize | Ladderize a Tree |
| latag2n | Leading and Trailing Alignment Gaps to N |
| lmorigin | Multiple regression through the origin |
| LTT | Theoretical Lineage-Through Time Plots |
| 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 |
| MoranI | Moran's I Autocorrelation Index |
| MPR | Most Parsimonious Reconstruction |
| 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... |
| node.dating | node.dating |
| node.depth | Depth and Heights of Nodes and Tips |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree |
| nodepath | Find Paths of Nodes |
| 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.phyloExtra | Extra Fuctions to Plot and Annotate Phylogenies |
| plotTreeTime | Plot Tree With Time Axis |
| plot.varcomp | Plot Variance Components |
| print.phylo | Compact Display of a Phylogeny |
| rDNAbin | Random DNA Sequences |
| 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.gff | Read GFF Files |
| 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 |
| reconstruct | Continuous Ancestral Character Estimation |
| 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 |
| rTraitCont | Continuous Character Simulation |
| rTraitDisc | Discrete Character Simulation |
| rTraitMult | Multivariate Character Simulation |
| rtree | Generate Random Trees |
| rtt | Root a Tree by Root-to-Tip Regression |
| SDM | Construction of Consensus Distance Matrix With SDM |
| 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 |
| solveAmbiguousBases | Solve Ambiguous Bases in DNA Sequences |
| 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 |
| trans | Translation from DNA to Amino Acid Sequences |
| treePop | Tree Popping |
| trex | Tree Explorer With Multiple Devices |
| triangMtd | Tree Reconstruction Based on the Triangles Method |
| unique.multiPhylo | Revomes Duplicate Trees |
| updateLabel | Update Labels |
| varcomp | Compute Variance Component Estimates |
| varCompPhylip | Variance Components with Orthonormal Contrasts |
| vcv2phylo | Variance-Covariance Matrix to Tree |
| vcv.phylo | 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 |
