ape v3.0-10
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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 | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| additive | Incomplete Distance Matrix Filling | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| MPR | Most Parsimonious Reconstruction | |
| alex | Alignment Explorer With Multiple Devices | |
| ape-internal | Internal Ape Functions | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| bd.time | Time-Dependent Birth-Death Models | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| coalescent.intervals | Coalescent Intervals | |
| bind.tree | Binds Trees | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| as.bitsplits | Conversion Among Split Classes | |
| is.binary.tree | Test for Binary Tree | |
| axisPhylo | Axis on Side of Phylogeny | |
| Moran.I | Moran's I Autocorrelation Index | |
| compar.cheverud | Cheverud's Comparative Method | |
| is.monophyletic | Is Group Monophyletic | |
| njs | Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* | |
| c.phylo | Building Lists of Trees | |
| chronos | Molecular Dating by Penalised Likelihood and Maximum Likelihood | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| chiroptera | Bat Phylogeny | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| yule | Fits the Yule Model to a Phylogenetic Tree | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| mat3 | Three Matrices | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| edges | Draw Additional Edges on a Plotted Tree | |
| mat5Mrand | Five Independent Trees | |
| write.tree | Write Tree File in Parenthetic Format | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| matexpo | Matrix Exponential | |
| ladderize | Ladderize a Tree | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| summary.phylo | Print Summary of a Phylogeny | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| pcoa | Principal Coordinate Analysis | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| read.nexus | Read Tree File in Nexus Format | |
| collapse.singles | Collapse Single Nodes | |
| clustal | Multiple Sequence Alignment with External Applications | |
| evonet | Evolutionary Networks | |
| plot.varcomp | Plot Variance Components | |
| corMartins | Martins's (1997) Correlation Structure | |
| rtree | Generates Random Trees | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| rTraitCont | Continuous Character Simulation | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| is.compatible | Check Compatibility of Splits | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| write.nexus.data | Write Character Data in NEXUS Format | |
| where | Find Patterns in DNA Sequences | |
| yule.time | Fits the Time-Dependent Yule Model | |
| ewLasso | Incomplete distances and edge weights of unrooted topology | |
| rTraitMult | Multivariate Character Simulation | |
| corBrownian | Brownian Correlation Structure | |
| triangMtd | Tree Reconstruction Based on the Triangles Method | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| multiphylo | Manipulating Lists of Trees | |
| which.edge | Identifies Edges of a Tree | |
| print.phylo | Compact Display of a Phylogeny | |
| write.nexus | Write Tree File in Nexus Format | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| as.phylo | Conversion Among Tree and Network Objects | |
| node.depth | Depth and Heights of Nodes and Tips | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| ltt.plot | Lineages Through Time Plot | |
| cherry | Number of Cherries and Null Models of Trees | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| base.freq | Base frequencies from DNA Sequences | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| read.caic | Read Tree File in CAIC Format | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| treePop | Tree Popping | |
| root | Roots Phylogenetic Trees | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| trex | Tree Explorer With Multiple Devices | |
| skylineplot | Drawing Skyline Plot Graphs | |
| SDM | Construction of Consensus Distance Matrix With SDM | |
| weight.taxo | Define Similarity Matrix | |
| speciesTree | Species Tree Estimation | |
| makeNodeLabel | Makes Node Labels | |
| zoom | Zoom on a Portion of a Phylogeny | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| makeLabel | Label Management | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| carnivora | Carnivora body sizes and life history traits | |
| compar.lynch | Lynch's Comparative Method | |
| nj | Neighbor-Joining Tree Estimation | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| consensus | Concensus Trees | |
| mvr | Minimum Variance Reduction | |
| pic | Phylogenetically Independent Contrasts | |
| corClasses | Phylogenetic Correlation Structures | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| stree | Generates Systematic Regular Trees | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| lmorigin | Multiple regression through the origin | |
| write.dna | Write DNA Sequences in a File | |
| read.dna | Read DNA Sequences in a File | |
| read.tree | Read Tree File in Parenthetic Format | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| opsin | Gene Tree of 32 opsin Sequences | |
| diversi.gof | Tests of Constant Diversification Rates | |
| multi2di | Collapse and Resolve Multichotomies | |
| mst | Minimum Spanning Tree | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| rotate | Swapping Sister Clades | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| varcomp | Compute Variance Component Estimates | |
| ace | Ancestral Character Estimation | |
| compar.gee | Comparative Analysis with GEEs | |
| CADM.global | Congruence among distance matrices | |
| reorder.phylo | Internal Reordering of Trees | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| phymltest | Fits a Bunch of Models with PhyML | |
| plot.phylo | Plot Phylogenies | |
| mat5M3ID | Five Trees | |
| plot.correlogram | Plot a Correlogram | |
| yule.cov | Fits the Yule Model With Covariates | |
| rTraitDisc | Discrete Character Simulation | |
| parafit | Test of host-parasite coevolution | |
| correlogram.formula | Phylogenetic Correlogram | |
| dist.gene | Pairwise Distances from Genetic Data | |
| delta.plot | Delta Plots | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| diversi.time | Analysis of Diversification with Survival Models | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| dist.topo | Topological Distances Between Two Trees | |
| data.nex | NEXUS Data Example | |
| dbd | Probability Density Under Birth--Death Models | |
| compute.brtime | Compute and Set Branching Times | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| compute.brlen | Branch Lengths Computation | |
| diversity.contrast.test | Diversity Contrast Test | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| No Results! | ||
Last month downloads
Details
| Date | 2013-09-09 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape-package.ird.fr/ |
| Packaged | 2013-09-10 03:41:27 UTC; paradis |
| NeedsCompilation | yes |
| Repository | CRAN |
| Date/Publication | 2013-09-10 08:01:18 |
| depends | base (>= 2.6.0) , R (>= 2.6.0) |
| 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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