ape v2.6-3
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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 | |
| diversi.gof | Tests of Constant Diversification Rates | |
| mat5M3ID | Five Trees | |
| plot.varcomp | Plot Variance Components | |
| parafit | Test of host-parasite coevolution | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| correlogram.formula | Phylogenetic Correlogram | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| compar.cheverud | Cheverud's Comparative Method | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| cherry | Number of Cherries and Null Models of Trees | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| consensus | Concensus Trees | |
| multiphylo | Manipulating Lists of Trees | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| pcoa | Principal Coordinate Analysis | |
| is.monophyletic | Is Group Monophyletic | |
| edges | Draw Additional Edges on a Plotted Tree | |
| MPR | Most Parsimonious Reconstruction | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| corBrownian | Brownian Correlation Structure | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| bind.tree | Binds Trees | |
| data.nex | NEXUS Data Example | |
| c.phylo | Building Lists of Trees | |
| diversi.time | Analysis of Diversification with Survival Models | |
| compute.brlen | Branch Lengths Computation | |
| plot.correlogram | Plot a Correlogram | |
| multi2di | Collapse and Resolve Multichotomies | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| write.dna | Write DNA Sequences in a File | |
| write.nexus | Write Tree File in Nexus Format | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| base.freq | Base frequencies from DNA Sequences | |
| dist.gene | Pairwise Distances from Genetic Data | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| dist.topo | Topological Distances Between Two Trees | |
| opsin | Gene Tree of 32 opsin Sequences | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| Moran.I | Moran's I Autocorrelation Index | |
| corClasses | Phylogenetic Correlation Structures | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| collapse.singles | Collapse Single Nodes | |
| carnivora | Carnivora body sizes and life history traits | |
| GC.content | Content in GC from DNA Sequences | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| as.phylo | Conversion Among Tree Objects | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| corMartins | Martins's (1997) Correlation Structure | |
| CADM.global | Congruence among distance matrices | |
| read.dna | Read DNA Sequences in a File | |
| varcomp | Compute Variance Component Estimates | |
| mat5Mrand | Five Independent Trees | |
| mat3 | Three Matrices | |
| ape-defunct | Defunct Ape Functions | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| is.binary.tree | Test for Binary Tree | |
| compar.lynch | Lynch's Comparative Method | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| ladderize | Ladderize a Tree | |
| read.caic | Read Tree File in CAIC Format | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| ace | Ancestral Character Estimation | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| which.edge | Identifies Edges of a Tree | |
| makeNodeLabel | Makes Node Labels | |
| reorder.phylo | Internal Reordering of Trees | |
| stree | Generates Systematic Regular Trees | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| nj | Neighbor-Joining Tree Estimation | |
| speciesTree | Species Tree Estimation | |
| rotate | Swapping sister clades | |
| rTraitDisc | Discrete Character Simulation | |
| compar.gee | Comparative Analysis with GEEs | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| lmorigin | Multiple regression through the origin | |
| rTraitCont | Continuous Character Simulation | |
| write.tree | Write Tree File in Parenthetic Format | |
| read.tree | Read Tree File in Parenthetic Format | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| axisPhylo | Axis on Side of Phylogeny | |
| ape-internal | Internal Ape Functions | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| chiroptera | Bat Phylogeny | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| coalescent.intervals | Coalescent Intervals | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| delta.plot | Delta Plots | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| weight.taxo | Define Similarity Matrix | |
| root | Roots Phylogenetic Trees | |
| node.depth | Depth of Nodes and Tips | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| mst | Minimum Spanning Tree | |
| phymltest | Fits a Bunch of Models with PhyML | |
| skylineplot | Drawing Skyline Plot Graphs | |
| yule.time | Fits the Time-Dependent Yule Model | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| yule.cov | Fits the Yule Model With Covariates | |
| print.phylo | Compact Display of a Phylogeny | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| makeLabel | Label Management | |
| ltt.plot | Lineages Through Time Plot | |
| summary.phylo | Print Summary of a Phylogeny | |
| pic | Phylogenetically Independent Contrasts | |
| matexpo | Matrix Exponential | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| read.nexus | Read Tree File in Nexus Format | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| plot.phylo | Plot Phylogenies | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| rtree | Generates Random Trees | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| bd.time | Time-Dependent Birth-Death Models | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| zoom | Zoom on a Portion of a Phylogeny | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| No Results! | ||
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Details
| Date | 2011-02-17 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2011-02-18 04:19:45 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2011-02-18 17:29:37 |
| 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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