ape v2.7-3
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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, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree,
generalized skyline plots, estimation of absolute evolutionary
rates and clock-like trees using mean path lengths,
non-parametric rate smoothing and penalized likelihood.
Phylogeny estimation can be done with the NJ, BIONJ, and ME
methods.
Functions in ape
| Name | Description | |
| rTraitDisc | Discrete Character Simulation | |
| MPR | Most Parsimonious Reconstruction | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| compute.brlen | Branch Lengths Computation | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| chiroptera | Bat Phylogeny | |
| compar.cheverud | Cheverud's Comparative Method | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| base.freq | Base frequencies from DNA Sequences | |
| corBrownian | Brownian Correlation Structure | |
| ape-internal | Internal Ape Functions | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| ape-defunct | Defunct Ape Functions | |
| cherry | Number of Cherries and Null Models of Trees | |
| compar.gee | Comparative Analysis with GEEs | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| coalescent.intervals | Coalescent Intervals | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| axisPhylo | Axis on Side of Phylogeny | |
| is.monophyletic | Is Group Monophyletic | |
| c.phylo | Building Lists of Trees | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| compar.lynch | Lynch's Comparative Method | |
| bind.tree | Binds Trees | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| as.phylo | Conversion Among Tree and Network Objects | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| node.depth | Depth of Nodes and Tips | |
| reorder.phylo | Internal Reordering of Trees | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| corClasses | Phylogenetic Correlation Structures | |
| clustal | Multiple Sequence Alignment with External Applications | |
| diversity.contrast.test | Diversity Contrast Test | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| plot.varcomp | Plot Variance Components | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| opsin | Gene Tree of 32 opsin Sequences | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| zoom | Zoom on a Portion of a Phylogeny | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| makeLabel | Label Management | |
| dist.gene | Pairwise Distances from Genetic Data | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| write.dna | Write DNA Sequences in a File | |
| lmorigin | Multiple regression through the origin | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| mst | Minimum Spanning Tree | |
| mat5M3ID | Five Trees | |
| diversi.gof | Tests of Constant Diversification Rates | |
| GC.content | Content in GC from DNA Sequences | |
| yule | Fits the Yule Model to a Phylogenetic Tree | |
| varcomp | Compute Variance Component Estimates | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| read.tree | Read Tree File in Parenthetic Format | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| read.caic | Read Tree File in CAIC Format | |
| phymltest | Fits a Bunch of Models with PhyML | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| rotate | Swapping sister clades | |
| mat3 | Three Matrices | |
| delta.plot | Delta Plots | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| evonet | Evolutionary Networks | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| write.tree | Write Tree File in Parenthetic Format | |
| print.phylo | Compact Display of a Phylogeny | |
| write.nexus | Write Tree File in Nexus Format | |
| Moran.I | Moran's I Autocorrelation Index | |
| skylineplot | Drawing Skyline Plot Graphs | |
| read.dna | Read DNA Sequences in a File | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| ltt.plot | Lineages Through Time Plot | |
| makeNodeLabel | Makes Node Labels | |
| which.edge | Identifies Edges of a Tree | |
| pcoa | Principal Coordinate Analysis | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| root | Roots Phylogenetic Trees | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| data.nex | NEXUS Data Example | |
| speciesTree | Species Tree Estimation | |
| ace | Ancestral Character Estimation | |
| parafit | Test of host-parasite coevolution | |
| nj | Neighbor-Joining Tree Estimation | |
| plot.phylo | Plot Phylogenies | |
| dist.topo | Topological Distances Between Two Trees | |
| corMartins | Martins's (1997) Correlation Structure | |
| stree | Generates Systematic Regular Trees | |
| diversi.time | Analysis of Diversification with Survival Models | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| summary.phylo | Print Summary of a Phylogeny | |
| multi2di | Collapse and Resolve Multichotomies | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| carnivora | Carnivora body sizes and life history traits | |
| correlogram.formula | Phylogenetic Correlogram | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| yule.cov | Fits the Yule Model With Covariates | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| pic | Phylogenetically Independent Contrasts | |
| ladderize | Ladderize a Tree | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| consensus | Concensus Trees | |
| compute.brtime | Compute and Set Branching Times | |
| trex | Tree Explorer With Multiple Devices | |
| is.binary.tree | Test for Binary Tree | |
| multiphylo | Manipulating Lists of Trees | |
| bd.time | Time-Dependent Birth-Death Models | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| mat5Mrand | Five Independent Trees | |
| CADM.global | Congruence among distance matrices | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| matexpo | Matrix Exponential | |
| rtree | Generates Random Trees | |
| weight.taxo | Define Similarity Matrix | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| yule.time | Fits the Time-Dependent Yule Model | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| read.nexus | Read Tree File in Nexus Format | |
| edges | Draw Additional Edges on a Plotted Tree | |
| collapse.singles | Collapse Single Nodes | |
| rTraitMult | Multivariate Character Simulation | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| rTraitCont | Continuous Character Simulation | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| plot.correlogram | Plot a Correlogram | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| No Results! | ||
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Details
| Date | 2011-08-08 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2011-08-08 14:48:09 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2011-08-09 04:59:01 |
| depends | base (>= 2.6.0) , R (>= 2.6.0) |
| imports | gee , lattice , nlme |
| Contributors | Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Klaus Schliep, Korbinian Strimmer, Damien Vienne |
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