ape v2.5-3
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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 | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| ape-internal | Internal Ape Functions | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| cherry | Number of Cherries and Null Models of Trees | |
| ape-defunct | Defunct Ape Functions | |
| c.phylo | Building Lists of Trees | |
| bind.tree | Binds Trees | |
| Moran.I | Moran's I Autocorrelation Index | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| chiroptera | Bat Phylogeny | |
| compute.brlen | Branch Lengths Computation | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| matexpo | Matrix Exponential | |
| data.nex | NEXUS Data Example | |
| GC.content | Content in GC from DNA Sequences | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| corBrownian | Brownian Correlation Structure | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| axisPhylo | Axis on Side of Phylogeny | |
| opsin | Gene Tree of 32 opsin Sequences | |
| coalescent.intervals | Coalescent Intervals | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| consensus | Concensus Trees | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| as.phylo | Conversion Among Tree Objects | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| collapse.singles | Collapse Single Nodes | |
| compar.cheverud | Cheverud's Comparative Method | |
| corClasses | Phylogenetic Correlation Structures | |
| carnivora | Carnivora body sizes and life history traits | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| base.freq | Base frequencies from DNA Sequences | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| correlogram.formula | Phylogenetic Correlogram | |
| ace | Ancestral Character Estimation | |
| corMartins | Martins's (1997) Correlation Structure | |
| dist.gene | Pairwise Distances from Genetic Data | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| compar.gee | Comparative Analysis with GEEs | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| compar.lynch | Lynch's Comparative Method | |
| delta.plot | Delta Plots | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| diversi.time | Analysis of Diversification with Survival Models | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| reorder.phylo | Internal Reordering of Trees | |
| rtree | Generates Random Trees | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| yule.time | Fits the Time-Dependent Yule Model | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| pic | Phylogenetically Independent Contrasts | |
| read.caic | Read Tree File in CAIC Format | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| plot.varcomp | Plot Variance Components | |
| skylineplot | Drawing Skyline Plot Graphs | |
| zoom | Zoom on a Portion of a Phylogeny | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| read.dna | Read DNA Sequences in a File | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| phymltest | Fits a Bunch of Models with PhyML | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| parafit | Test of host-parasite coevolution | |
| plot.phylo | Plot Phylogenies | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| CADM.global | Congruence among distance matrices | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| is.binary.tree | Test for Binary Tree | |
| is.monophyletic | Is Group Monophyletic | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| diversi.gof | Tests of Constant Diversification Rates | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| makeLabel | Label Management | |
| edges | Draw Additional Edges on a Plotted Tree | |
| makeNodeLabel | Makes Node Labels | |
| dist.topo | Topological Distances Between Two Trees | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| node.depth | Depth of Nodes and Tips | |
| nj | Neighbor-Joining Tree Estimation | |
| mst | Minimum Spanning Tree | |
| multiphylo | Manipulating Lists of Trees | |
| ladderize | Ladderize a Tree | |
| mat5Mrand | Five Independent Trees | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| lmorigin | Multiple regression through the origin | |
| pcoa | Principal Coordinate Analysis | |
| rTraitCont | Continuous Character Simulation | |
| stree | Generates Systematic Regular Trees | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| write.tree | Write Tree File in Parenthetic Format | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| read.tree | Read Tree File in Parenthetic Format | |
| yule.cov | Fits the Yule Model With Covariates | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| rTraitDisc | Discrete Character Simulation | |
| which.edge | Identifies Edges of a Tree | |
| write.dna | Write DNA Sequences in a File | |
| multi2di | Collapse and Resolve Multichotomies | |
| varcomp | Compute Variance Component Estimates | |
| mat3 | Three Matrices | |
| read.nexus | Read Tree File in Nexus Format | |
| mat5M3ID | Five Trees | |
| ltt.plot | Lineages Through Time Plot | |
| print.phylo | Compact Display of a Phylogeny | |
| plot.correlogram | Plot a Correlogram | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| weight.taxo | Define Similarity Matrix | |
| summary.phylo | Print Summary of a Phylogeny | |
| root | Roots Phylogenetic Trees | |
| write.nexus | Write Tree File in Nexus Format | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| rotate | Swapping sister clades | |
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Details
| Date | 2010-05-27 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2010-06-14 17:49:05 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2010-06-15 08:49:47 |
| 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 |
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