ape v2.5-1
0
Monthly downloads
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 | |
| as.phylo | Conversion Among Tree Objects | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| ape-defunct | Defunct Ape Functions | |
| data.nex | NEXUS Data Example | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| ladderize | Ladderize a Tree | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| read.caic | Read Tree File in CAIC Format | |
| delta.plot | Delta Plots | |
| compar.cheverud | Cheverud's Comparative Method | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| makeNodeLabel | Makes Node Labels | |
| diversi.gof | Tests of Constant Diversification Rates | |
| reorder.phylo | Internal Reordering of Trees | |
| ape-internal | Internal Ape Functions | |
| read.tree | Read Tree File in Parenthetic Format | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| rTraitCont | Continuous Character Simulation | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| diversi.time | Analysis of Diversification with Survival Models | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| CADM.global | Congruence among distance matrices | |
| Moran.I | Moran's I Autocorrelation Index | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| nj | Neighbor-Joining Tree Estimation | |
| corClasses | Phylogenetic Correlation Structures | |
| phymltest | Fits a Bunch of Models with PhyML | |
| dist.topo | Topological Distances Between Two Trees | |
| coalescent.intervals | Coalescent Intervals | |
| opsin | Gene Tree of 32 opsin Sequences | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| axisPhylo | Axis on Side of Phylogeny | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| evolve.phylo | Ancestral Character Simulation | |
| correlogram.formula | Phylogenetic Correlogram | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| ace | Ancestral Character Estimation | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| cherry | Number of Cherries and Null Models of Trees | |
| print.phylo | Compact Display of a Phylogeny | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| root | Roots Phylogenetic Trees | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| stree | Generates Systematic Regular Trees | |
| is.binary.tree | Test for Binary Tree | |
| compar.gee | Comparative Analysis with GEEs | |
| lmorigin | Multiple regression through the origin | |
| base.freq | Base frequencies from DNA Sequences | |
| which.edge | Identifies Edges of a Tree | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| chiroptera | Bat Phylogeny | |
| makeLabel | Label Management | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| plot.varcomp | Plot Variance Components | |
| parafit | Test of host-parasite coevolution | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| varcomp | Compute Variance Component Estimates | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| pcoa | Principal Coordinate Analysis | |
| yule.cov | Fits the Yule Model With Covariates | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| mat5M3ID | Five Trees | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| corBrownian | Brownian Correlation Structure | |
| collapse.singles | Collapse Single Nodes | |
| matexpo | Matrix Exponential | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| skylineplot | Drawing Skyline Plot Graphs | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| plot.phylo | Plot Phylogenies | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| yule.time | Fits the Time-Dependent Yule Model | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| carnivora | Carnivora body sizes and life history traits | |
| zoom | Zoom on a Portion of a Phylogeny | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| rtree | Generates Random Trees | |
| plot.correlogram | Plot a Correlogram | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| node.depth | Depth of Nodes and Tips | |
| ltt.plot | Lineages Through Time Plot | |
| consensus | Concensus Trees | |
| bind.tree | Binds Trees | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| rotate | Swapping sister clades | |
| edges | Draw Additional Edges on a Plotted Tree | |
| compar.lynch | Lynch's Comparative Method | |
| mst | Minimum Spanning Tree | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| summary.phylo | Print Summary of a Phylogeny | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| read.dna | Read DNA Sequences in a File | |
| write.tree | Write Tree File in Parenthetic Format | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| compute.brlen | Branch Lengths Computation | |
| read.nexus | Read Tree File in Nexus Format | |
| write.dna | Write DNA Sequences in a File | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| is.monophyletic | Is Group Monophyletic | |
| mat5Mrand | Five Independent Trees | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| pic | Phylogenetically Independent Contrasts | |
| rTraitDisc | Discrete Character Simulation | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| GC.content | Content in GC from DNA Sequences | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| corMartins | Martins's (1997) Correlation Structure | |
| dist.gene | Pairwise Distances from Genetic Data | |
| mat3 | Three Matrices | |
| multi2di | Collapse and Resolve Multichotomies | |
| weight.taxo | Define Similarity Matrix | |
| write.nexus | Write Tree File in Nexus Format | |
| multiphylo | Manipulating Lists of Trees | |
| c.phylo | Building Lists of Trees | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| No Results! | ||
Last month downloads
Details
| Date | 2010-03-29 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2010-03-29 14:06:55 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2010-04-06 17:12:33 |
| 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, Korbinian Strimmer, Damien Vienne, Gangolf Jobb |
Include our badge in your README
[](http://www.rdocumentation.org/packages/ape)