ape v3.4
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Analyses of Phylogenetics and Evolution
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Functions in ape
| Name | Description | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| additive | Incomplete Distance Matrix Filling | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| as.phylo | Conversion Among Tree and Network Objects | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| binaryPGLMM | Phylogenetic Generalized Linear Mixed Model for Binary Data | |
| alview | Print DNA Sequence Alignements | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| checkValidPhylo | Check the Structure of a "phylo" Object | |
| DNAbin2indel | Recode Blocks of Indels | |
| chiroptera | Bat Phylogeny | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| compar.gee | Comparative Analysis with GEEs | |
| Moran.I | Moran's I Autocorrelation Index | |
| edges | Draw Additional Edges on a Plotted Tree | |
| dbd | Probability Density Under Birth--Death Models | |
| makeNodeLabel | Makes Node Labels | |
| corphylo | Correlations among Multiple Traits with Phylogenetic Signal | |
| carnivora | Carnivora body sizes and life history traits | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| bind.tree | Binds Trees | |
| compar.lynch | Lynch's Comparative Method | |
| alex | Alignment Explorer With Multiple Devices | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| coalescent.intervals | Coalescent Intervals | |
| axisPhylo | Axis on Side of Phylogeny | |
| reorder.phylo | Internal Reordering of Trees | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| chronos | Molecular Dating by Penalised Likelihood and Maximum Likelihood | |
| bd.time | Time-Dependent Birth-Death Models | |
| corMartins | Martins's (1997) Correlation Structure | |
| compute.brlen | Branch Lengths Computation | |
| collapse.singles | Collapse Single Nodes | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| diversi.time | Analysis of Diversification with Survival Models | |
| ladderize | Ladderize a Tree | |
| clustal | Multiple Sequence Alignment with External Applications | |
| consensus | Concensus Trees | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| ace | Ancestral Character Estimation | |
| node.depth | Depth and Heights of Nodes and Tips | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| as.bitsplits | Split Frequencies and Conversion Among Split Classes | |
| read.caic | Read Tree File in CAIC Format | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| multi2di | Collapse and Resolve Multichotomies | |
| ewLasso | Incomplete distances and edge weights of unrooted topology | |
| SDM | Construction of Consensus Distance Matrix With SDM | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| corBrownian | Brownian Correlation Structure | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| data.nex | NEXUS Data Example | |
| trex | Tree Explorer With Multiple Devices | |
| read.nexus | Read Tree File in Nexus Format | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| rTraitCont | Continuous Character Simulation | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| opsin | Gene Tree of 32 opsin Sequences | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| label2table | Label Management | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| is.binary.tree | Test for Binary Tree | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| plot.correlogram | Plot a Correlogram | |
| matexpo | Matrix Exponential | |
| c.phylo | Building Lists of Trees | |
| CADM.global | Congruence among distance matrices | |
| dist.gene | Pairwise Distances from Genetic Data | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| ape-internal | Internal Ape Functions | |
| mat3 | Three Matrices | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| rtree | Generates Random Trees | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| print.phylo | Compact Display of a Phylogeny | |
| write.dna | Write DNA Sequences in a File | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| corClasses | Phylogenetic Correlation Structures | |
| mst | Minimum Spanning Tree | |
| which.edge | Identifies Edges of a Tree | |
| zoom | Zoom on a Portion of a Phylogeny | |
| skylineplot | Drawing Skyline Plot Graphs | |
| ltt.plot | Lineages Through Time Plot | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| triangMtd | Tree Reconstruction Based on the Triangles Method | |
| speciesTree | Species Tree Estimation | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| diversi.gof | Tests of Constant Diversification Rates | |
| summary.phylo | Print Summary of a Phylogeny | |
| mvr | Minimum Variance Reduction | |
| multiphylo | Manipulating Lists of Trees | |
| vcv2phylo | Variance-Covariance Matrix to Tree | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| is.monophyletic | Is Group Monophyletic | |
| yule.time | Fits the Time-Dependent Yule Model | |
| read.dna | Read DNA Sequences in a File | |
| where | Find Patterns in DNA Sequences | |
| write.tree | Write Tree File in Parenthetic Format | |
| nodepath | Find Paths of Nodes | |
| write.nexus.data | Write Character Data in NEXUS Format | |
| delta.plot | Delta Plots | |
| cherry | Number of Cherries and Null Models of Trees | |
| is.compatible | Check Compatibility of Splits | |
| pic | Phylogenetically Independent Contrasts | |
| treePop | Tree Popping | |
| base.freq | Base frequencies from DNA Sequences | |
| rTraitMult | Multivariate Character Simulation | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| phymltest | Fits a Bunch of Models with PhyML | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| write.nexus | Write Tree File in Nexus Format | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| mat5Mrand | Five Independent Trees | |
| MPR | Most Parsimonious Reconstruction | |
| plot.phylo | Plot Phylogenies | |
| read.tree | Read Tree File in Parenthetic Format | |
| diversity.contrast.test | Diversity Contrast Test | |
| evonet | Evolutionary Networks | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| makeLabel | Label Management | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| plot.varcomp | Plot Variance Components | |
| lmorigin | Multiple regression through the origin | |
| rTraitDisc | Discrete Character Simulation | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| reconstruct | Continuous Ancestral Character Estimation | |
| stree | Generates Systematic Regular Trees | |
| yule.cov | Fits the Yule Model With Covariates | |
| rtt | Root a Tree by Root-to-Tip Regression | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| nj | Neighbor-Joining Tree Estimation | |
| compute.brtime | Compute and Set Branching Times | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| phydataplot | Tree Annotation | |
| varcomp | Compute Variance Component Estimates | |
| rotate | Swapping Sister Clades | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| def | Definition of Vectors for Plotting or Annotating | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| mat5M3ID | Five Trees | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| compar.cheverud | Cheverud's Comparative Method | |
| pcoa | Principal Coordinate Analysis | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| parafit | Test of host-parasite coevolution | |
| njs | Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* | |
| correlogram.formula | Phylogenetic Correlogram | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| weight.taxo | Define Similarity Matrix | |
| yule | Fits the Yule Model to a Phylogenetic Tree | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| LTT | Theoretical Lineage-Through Time Plots | |
| dist.topo | Topological Distances Between Two Trees | |
| root | Roots Phylogenetic Trees | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
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Details
| Date | 2015-11-29 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape-package.ird.fr/ |
| NeedsCompilation | yes |
| Packaged | 2015-11-29 08:54:16 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2015-11-29 19:14:31 |
| depends | base (>= 3.0.0) , R (>= 3.0.0) |
| suggests | expm , gee |
| imports | graphics , lattice , methods , nlme , parallel , stats , tools , utils |
| Contributors | Anthony Ives, Emmanuel Paradis, Ben Bolker, Julien Claude, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Hoa Sien Cuong, Damien de Vienne, Rosemary McCloskey, Simon Blomberg, Gilles Didier, Manuela Royer-Carenzi |
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