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Analyses of Phylogenetics and Evolution
ape provides 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 | |
| carnivora | Carnivora body sizes and life history traits | |
| makeLabel | Label Management | |
| c.phylo | Building Lists of Trees | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| compar.gee | Comparative Analysis with GEEs | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| diversi.gof | Tests of Constant Diversification Rates | |
| as.phylo | Conversion Among Tree and Network Objects | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| njs | Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* | |
| write.tree | Write Tree File in Parenthetic Format | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| MPR | Most Parsimonious Reconstruction | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| mat5M3ID | Five Trees | |
| mat5Mrand | Five Independent Trees | |
| corClasses | Phylogenetic Correlation Structures | |
| plot.varcomp | Plot Variance Components | |
| delta.plot | Delta Plots | |
| stree | Generates Systematic Regular Trees | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| speciesTree | Species Tree Estimation | |
| cherry | Number of Cherries and Null Models of Trees | |
| SDM | Construction of Consensus Distance Matrix With SDM | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| is.binary.tree | Test for Binary Tree | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| CADM.global | Congruence among distance matrices | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| mst | Minimum Spanning Tree | |
| phymltest | Fits a Bunch of Models with PhyML | |
| opsin | Gene Tree of 32 opsin Sequences | |
| matexpo | Matrix Exponential | |
| def | Definition of Vectors for Plotting or Annotating | |
| edges | Draw Additional Edges on a Plotted Tree | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| weight.taxo | Define Similarity Matrix | |
| mvr | Minimum Variance Reduction | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| ace | Ancestral Character Estimation | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| nodepath | Find Paths of Nodes | |
| alex | Alignment Explorer With Multiple Devices | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| ape-internal | Internal Ape Functions | |
| plot.correlogram | Plot a Correlogram | |
| base.freq | Base frequencies from DNA Sequences | |
| rtree | Generates Random Trees | |
| chronos | Molecular Dating by Penalised Likelihood and Maximum Likelihood | |
| corBrownian | Brownian Correlation Structure | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| rTraitCont | Continuous Character Simulation | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| data.nex | NEXUS Data Example | |
| zoom | Zoom on a Portion of a Phylogeny | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| reorder.phylo | Internal Reordering of Trees | |
| diversity.contrast.test | Diversity Contrast Test | |
| varcomp | Compute Variance Component Estimates | |
| rTraitDisc | Discrete Character Simulation | |
| lmorigin | Multiple regression through the origin | |
| write.dna | Write DNA Sequences in a File | |
| root | Roots Phylogenetic Trees | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| skylineplot | Drawing Skyline Plot Graphs | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| trex | Tree Explorer With Multiple Devices | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| write.nexus | Write Tree File in Nexus Format | |
| node.depth | Depth and Heights of Nodes and Tips | |
| nj | Neighbor-Joining Tree Estimation | |
| rotate | Swapping Sister Clades | |
| plot.phylo | Plot Phylogenies | |
| rTraitMult | Multivariate Character Simulation | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| consensus | Concensus Trees | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| compar.cheverud | Cheverud's Comparative Method | |
| compar.lynch | Lynch's Comparative Method | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| dbd | Probability Density Under Birth--Death Models | |
| ltt.plot | Lineages Through Time Plot | |
| mat3 | Three Matrices | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| axisPhylo | Axis on Side of Phylogeny | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| write.nexus.data | Write Character Data in NEXUS Format | |
| print.phylo | Compact Display of a Phylogeny | |
| reconstruct | Continuous Ancestral Character Estimation | |
| yule | Fits the Yule Model to a Phylogenetic Tree | |
| Moran.I | Moran's I Autocorrelation Index | |
| triangMtd | Tree Reconstruction Based on the Triangles Method | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| bd.time | Time-Dependent Birth-Death Models | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| yule.cov | Fits the Yule Model With Covariates | |
| ladderize | Ladderize a Tree | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| diversi.time | Analysis of Diversification with Survival Models | |
| as.bitsplits | Split Frequencies and Conversion Among Split Classes | |
| phydataplot | Tree Annotation | |
| dist.topo | Topological Distances Between Two Trees | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| compute.brtime | Compute and Set Branching Times | |
| correlogram.formula | Phylogenetic Correlogram | |
| multiphylo | Manipulating Lists of Trees | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| is.monophyletic | Is Group Monophyletic | |
| LTT | Theoretical Lineage-Through Time Plots | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| treePop | Tree Popping | |
| pcoa | Principal Coordinate Analysis | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| read.dna | Read DNA Sequences in a File | |
| bind.tree | Binds Trees | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| read.caic | Read Tree File in CAIC Format | |
| read.tree | Read Tree File in Parenthetic Format | |
| read.nexus | Read Tree File in Nexus Format | |
| clustal | Multiple Sequence Alignment with External Applications | |
| where | Find Patterns in DNA Sequences | |
| yule.time | Fits the Time-Dependent Yule Model | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| rtt | Root a Tree by Root-to-Tip Regression | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| which.edge | Identifies Edges of a Tree | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| pic | Phylogenetically Independent Contrasts | |
| vcv2phylo | Variance-Covariance Matrix to Tree | |
| summary.phylo | Print Summary of a Phylogeny | |
| additive | Incomplete Distance Matrix Filling | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| coalescent.intervals | Coalescent Intervals | |
| compute.brlen | Branch Lengths Computation | |
| dist.gene | Pairwise Distances from Genetic Data | |
| ewLasso | Incomplete distances and edge weights of unrooted topology | |
| multi2di | Collapse and Resolve Multichotomies | |
| collapse.singles | Collapse Single Nodes | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| makeNodeLabel | Makes Node Labels | |
| chiroptera | Bat Phylogeny | |
| corMartins | Martins's (1997) Correlation Structure | |
| evonet | Evolutionary Networks | |
| is.compatible | Check Compatibility of Splits | |
| parafit | Test of host-parasite coevolution | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| No Results! | ||
Last month downloads
Details
| Date | 2014-12-05 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape-package.ird.fr/ |
| Packaged | 2014-12-04 21:10:22 UTC; paradis |
| NeedsCompilation | yes |
| Repository | CRAN |
| Date/Publication | 2014-12-05 17:18:03 |
| depends | base (>= 3.0.0) , R (>= 3.0.0) |
| suggests | expm , gee |
| imports | graphics , lattice , nlme , parallel , stats , tools , utils |
| Contributors | 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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