ape v3.1-1
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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, 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 | |
| additive | Incomplete Distance Matrix Filling | |
| mat5M3ID | Five Trees | |
| lmorigin | Multiple regression through the origin | |
| compar.cheverud | Cheverud's Comparative Method | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| is.compatible | Check Compatibility of Splits | |
| nj | Neighbor-Joining Tree Estimation | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| is.monophyletic | Is Group Monophyletic | |
| base.freq | Base frequencies from DNA Sequences | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| multi2di | Collapse and Resolve Multichotomies | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| plot.correlogram | Plot a Correlogram | |
| consensus | Concensus Trees | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| delta.plot | Delta Plots | |
| phydataplot | Tree Annotation | |
| root | Roots Phylogenetic Trees | |
| MPR | Most Parsimonious Reconstruction | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| correlogram.formula | Phylogenetic Correlogram | |
| dbd | Probability Density Under Birth--Death Models | |
| Moran.I | Moran's I Autocorrelation Index | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| edges | Draw Additional Edges on a Plotted Tree | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| cherry | Number of Cherries and Null Models of Trees | |
| bind.tree | Binds Trees | |
| ace | Ancestral Character Estimation | |
| axisPhylo | Axis on Side of Phylogeny | |
| diversi.gof | Tests of Constant Diversification Rates | |
| clustal | Multiple Sequence Alignment with External Applications | |
| bd.time | Time-Dependent Birth-Death Models | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| rTraitDisc | Discrete Character Simulation | |
| ladderize | Ladderize a Tree | |
| diversi.time | Analysis of Diversification with Survival Models | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| rTraitMult | Multivariate Character Simulation | |
| makeLabel | Label Management | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| corClasses | Phylogenetic Correlation Structures | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| ewLasso | Incomplete distances and edge weights of unrooted topology | |
| summary.phylo | Print Summary of a Phylogeny | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| diversity.contrast.test | Diversity Contrast Test | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| dist.gene | Pairwise Distances from Genetic Data | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| write.nexus.data | Write Character Data in NEXUS Format | |
| ape-internal | Internal Ape Functions | |
| triangMtd | Tree Reconstruction Based on the Triangles Method | |
| compute.brtime | Compute and Set Branching Times | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| carnivora | Carnivora body sizes and life history traits | |
| reorder.phylo | Internal Reordering of Trees | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| LTT | Theoretical Lineage-Through Time Plots | |
| corBrownian | Brownian Correlation Structure | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| rotate | Swapping Sister Clades | |
| chiroptera | Bat Phylogeny | |
| chronos | Molecular Dating by Penalised Likelihood and Maximum Likelihood | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| rTraitCont | Continuous Character Simulation | |
| read.caic | Read Tree File in CAIC Format | |
| parafit | Test of host-parasite coevolution | |
| is.binary.tree | Test for Binary Tree | |
| compar.gee | Comparative Analysis with GEEs | |
| yule | Fits the Yule Model to a Phylogenetic Tree | |
| c.phylo | Building Lists of Trees | |
| matexpo | Matrix Exponential | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| print.phylo | Compact Display of a Phylogeny | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| read.nexus | Read Tree File in Nexus Format | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| collapse.singles | Collapse Single Nodes | |
| corMartins | Martins's (1997) Correlation Structure | |
| mat5Mrand | Five Independent Trees | |
| coalescent.intervals | Coalescent Intervals | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| ltt.plot | Lineages Through Time Plot | |
| zoom | Zoom on a Portion of a Phylogeny | |
| makeNodeLabel | Makes Node Labels | |
| speciesTree | Species Tree Estimation | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| yule.time | Fits the Time-Dependent Yule Model | |
| multiphylo | Manipulating Lists of Trees | |
| read.dna | Read DNA Sequences in a File | |
| varcomp | Compute Variance Component Estimates | |
| write.dna | Write DNA Sequences in a File | |
| as.bitsplits | Split Frequencies and Conversion Among Split Classes | |
| where | Find Patterns in DNA Sequences | |
| treePop | Tree Popping | |
| which.edge | Identifies Edges of a Tree | |
| opsin | Gene Tree of 32 opsin Sequences | |
| rtree | Generates Random Trees | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| yule.cov | Fits the Yule Model With Covariates | |
| plot.varcomp | Plot Variance Components | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| stree | Generates Systematic Regular Trees | |
| data.nex | NEXUS Data Example | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| write.tree | Write Tree File in Parenthetic Format | |
| write.nexus | Write Tree File in Nexus Format | |
| evonet | Evolutionary Networks | |
| pic | Phylogenetically Independent Contrasts | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| read.tree | Read Tree File in Parenthetic Format | |
| mat3 | Three Matrices | |
| CADM.global | Congruence among distance matrices | |
| pcoa | Principal Coordinate Analysis | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| weight.taxo | Define Similarity Matrix | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| as.phylo | Conversion Among Tree and Network Objects | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| dist.topo | Topological Distances Between Two Trees | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| compute.brlen | Branch Lengths Computation | |
| plot.phylo | Plot Phylogenies | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| mst | Minimum Spanning Tree | |
| node.depth | Depth and Heights of Nodes and Tips | |
| skylineplot | Drawing Skyline Plot Graphs | |
| njs | Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* | |
| phymltest | Fits a Bunch of Models with PhyML | |
| mvr | Minimum Variance Reduction | |
| SDM | Construction of Consensus Distance Matrix With SDM | |
| alex | Alignment Explorer With Multiple Devices | |
| trex | Tree Explorer With Multiple Devices | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| compar.lynch | Lynch's Comparative Method | |
| rtt | Root a Tree by Root-to-Tip Regression | |
| No Results! | ||
Last month downloads
Details
| Date | 2014-03-06 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape-package.ird.fr/ |
| Packaged | 2014-03-10 19:32:32 UTC; paradis |
| NeedsCompilation | yes |
| Repository | CRAN |
| Date/Publication | 2014-03-11 08:49:37 |
| depends | base (>= 3.0.0) , R (>= 3.0.0) |
| suggests | expm , gee |
| imports | graphics , lattice , nlme , 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 |
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