ape v2.7-1
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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, 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 | |
| cherry | Number of Cherries and Null Models of Trees | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| GC.content | Content in GC from DNA Sequences | |
| clustal | Multiple Sequence Alignment with External Applications | |
| ape-internal | Internal Ape Functions | |
| collapse.singles | Collapse Single Nodes | |
| corClasses | Phylogenetic Correlation Structures | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| c.phylo | Building Lists of Trees | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| mst | Minimum Spanning Tree | |
| as.phylo | Conversion Among Tree and Network Objects | |
| coalescent.intervals | Coalescent Intervals | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| Moran.I | Moran's I Autocorrelation Index | |
| base.freq | Base frequencies from DNA Sequences | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| CADM.global | Congruence among distance matrices | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| edges | Draw Additional Edges on a Plotted Tree | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| chiroptera | Bat Phylogeny | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| summary.phylo | Print Summary of a Phylogeny | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| ape-defunct | Defunct Ape Functions | |
| consensus | Concensus Trees | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| carnivora | Carnivora body sizes and life history traits | |
| lmorigin | Multiple regression through the origin | |
| correlogram.formula | Phylogenetic Correlogram | |
| compute.brlen | Branch Lengths Computation | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| corBrownian | Brownian Correlation Structure | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| bd.time | Time-Dependent Birth-Death Models | |
| ace | Ancestral Character Estimation | |
| nj | Neighbor-Joining Tree Estimation | |
| write.nexus | Write Tree File in Nexus Format | |
| bind.tree | Binds Trees | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| compar.cheverud | Cheverud's Comparative Method | |
| write.tree | Write Tree File in Parenthetic Format | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| pic | Phylogenetically Independent Contrasts | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| dist.gene | Pairwise Distances from Genetic Data | |
| dist.topo | Topological Distances Between Two Trees | |
| diversity.contrast.test | Diversity Contrast Test | |
| compar.gee | Comparative Analysis with GEEs | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| makeNodeLabel | Makes Node Labels | |
| write.dna | Write DNA Sequences in a File | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| diversi.time | Analysis of Diversification with Survival Models | |
| opsin | Gene Tree of 32 opsin Sequences | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| matexpo | Matrix Exponential | |
| plot.correlogram | Plot a Correlogram | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| phymltest | Fits a Bunch of Models with PhyML | |
| parafit | Test of host-parasite coevolution | |
| makeLabel | Label Management | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| ladderize | Ladderize a Tree | |
| yule.cov | Fits the Yule Model With Covariates | |
| which.edge | Identifies Edges of a Tree | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| weight.taxo | Define Similarity Matrix | |
| is.monophyletic | Is Group Monophyletic | |
| delta.plot | Delta Plots | |
| ltt.plot | Lineages Through Time Plot | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| mat5M3ID | Five Trees | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| multiphylo | Manipulating Lists of Trees | |
| rTraitCont | Continuous Character Simulation | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| multi2di | Collapse and Resolve Multichotomies | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| zoom | Zoom on a Portion of a Phylogeny | |
| plot.phylo | Plot Phylogenies | |
| speciesTree | Species Tree Estimation | |
| corMartins | Martins's (1997) Correlation Structure | |
| is.binary.tree | Test for Binary Tree | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| data.nex | NEXUS Data Example | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| stree | Generates Systematic Regular Trees | |
| root | Roots Phylogenetic Trees | |
| read.dna | Read DNA Sequences in a File | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| read.nexus | Read Tree File in Nexus Format | |
| skylineplot | Drawing Skyline Plot Graphs | |
| read.tree | Read Tree File in Parenthetic Format | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| mat3 | Three Matrices | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| plot.varcomp | Plot Variance Components | |
| reorder.phylo | Internal Reordering of Trees | |
| rTraitDisc | Discrete Character Simulation | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| diversi.gof | Tests of Constant Diversification Rates | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| read.caic | Read Tree File in CAIC Format | |
| yule.time | Fits the Time-Dependent Yule Model | |
| rtree | Generates Random Trees | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| pcoa | Principal Coordinate Analysis | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| trex | Tree Explorer With Multiple Devices | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| print.phylo | Compact Display of a Phylogeny | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| MPR | Most Parsimonious Reconstruction | |
| varcomp | Compute Variance Component Estimates | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| compar.lynch | Lynch's Comparative Method | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| mat5Mrand | Five Independent Trees | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| axisPhylo | Axis on Side of Phylogeny | |
| node.depth | Depth of Nodes and Tips | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| rotate | Swapping sister clades | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| evonet | Evolutionary Networks | |
| rTraitMult | Multivariate Character Simulation | |
| compute.brtime | Compute and Set Branching Times | |
| No Results! | ||
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Details
| Date | 2011-03-26 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2011-03-26 08:36:10 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2011-03-26 16:04:05 |
| 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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