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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, ancestral character analyses,
analyses of diversification and macroevolution, computing
distances from allelic and nucleotide data, reading and writing
nucleotide sequences, and several tools such as Mantel's test,
minimum spanning tree, generalized skyline plots, graphical
exploration of phylogenetic data (alex, trex, kronoviz),
estimation of absolute evolutionary rates and clock-like trees
using mean path lengths and penalized likelihood. Phylogeny
estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
triangle methods, and several methods handling incomplete
distance matrices (NJ*, BIONJ*, MVR*, and the corresponding
triangle method). Some functions call external applications
(PhyML, Clustal, T-Coffee, Muscle) whose results are returned
into R.
Functions in ape
| Name | Description | |
| cherry | Number of Cherries and Null Models of Trees | |
| as.phylo | Conversion Among Tree and Network Objects | |
| diversi.time | Analysis of Diversification with Survival Models | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| MPR | Most Parsimonious Reconstruction | |
| Moran.I | Moran's I Autocorrelation Index | |
| SDM | Construction of Consensus Distance Matrix With SDM | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| additive | Incomplete Distance Matrix Filling | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| collapse.singles | Collapse Single Nodes | |
| compar.cheverud | Cheverud's Comparative Method | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| ape-internal | Internal Ape Functions | |
| carnivora | Carnivora body sizes and life history traits | |
| base.freq | Base frequencies from DNA Sequences | |
| dist.topo | Topological Distances Between Two Trees | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| diversi.gof | Tests of Constant Diversification Rates | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| consensus | Concensus Trees | |
| GC.content | Content in GC from DNA Sequences | |
| as.bitsplits | Conversion Among Split Classes | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| correlogram.formula | Phylogenetic Correlogram | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| compar.gee | Comparative Analysis with GEEs | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| stree | Generates Systematic Regular Trees | |
| plot.varcomp | Plot Variance Components | |
| corClasses | Phylogenetic Correlation Structures | |
| mat5M3ID | Five Trees | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| rTraitCont | Continuous Character Simulation | |
| write.dna | Write DNA Sequences in a File | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| clustal | Multiple Sequence Alignment with External Applications | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| nj | Neighbor-Joining Tree Estimation | |
| varcomp | Compute Variance Component Estimates | |
| read.nexus | Read Tree File in Nexus Format | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| treePop | Tree Popping | |
| write.nexus | Write Tree File in Nexus Format | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| is.binary.tree | Test for Binary Tree | |
| data.nex | NEXUS Data Example | |
| makeNodeLabel | Makes Node Labels | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| node.depth | Depth of Nodes and Tips | |
| is.monophyletic | Is Group Monophyletic | |
| plot.correlogram | Plot a Correlogram | |
| coalescent.intervals | Coalescent Intervals | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| ape-defunct | Defunct Ape Functions | |
| ladderize | Ladderize a Tree | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| alex | Alignment Explorer With Multiple Devices | |
| reorder.phylo | Internal Reordering of Trees | |
| multi2di | Collapse and Resolve Multichotomies | |
| which.edge | Identifies Edges of a Tree | |
| weight.taxo | Define Similarity Matrix | |
| speciesTree | Species Tree Estimation | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| read.dna | Read DNA Sequences in a File | |
| yule.time | Fits the Time-Dependent Yule Model | |
| multiphylo | Manipulating Lists of Trees | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| njs | Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* | |
| rtree | Generates Random Trees | |
| skylineplot | Drawing Skyline Plot Graphs | |
| read.caic | Read Tree File in CAIC Format | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| CADM.global | Congruence among distance matrices | |
| summary.phylo | Print Summary of a Phylogeny | |
| dist.gene | Pairwise Distances from Genetic Data | |
| print.phylo | Compact Display of a Phylogeny | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| opsin | Gene Tree of 32 opsin Sequences | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| makeLabel | Label Management | |
| matexpo | Matrix Exponential | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| axisPhylo | Axis on Side of Phylogeny | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| dbd | Probability Density Under Birth--Death Models | |
| zoom | Zoom on a Portion of a Phylogeny | |
| is.compatible | Check Compatibility of Splits | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| plot.phylo | Plot Phylogenies | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| chiroptera | Bat Phylogeny | |
| mat3 | Three Matrices | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| c.phylo | Building Lists of Trees | |
| rotate | Swapping sister clades | |
| ace | Ancestral Character Estimation | |
| delta.plot | Delta Plots | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| ltt.plot | Lineages Through Time Plot | |
| triangMtd | Tree Reconstruction Based on the Triangles Method | |
| yule | Fits the Yule Model to a Phylogenetic Tree | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| compar.lynch | Lynch's Comparative Method | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| corMartins | Martins's (1997) Correlation Structure | |
| write.tree | Write Tree File in Parenthetic Format | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| bind.tree | Binds Trees | |
| compute.brtime | Compute and Set Branching Times | |
| corBrownian | Brownian Correlation Structure | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| pic | Phylogenetically Independent Contrasts | |
| mvr | Minimum Variance Reduction | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| edges | Draw Additional Edges on a Plotted Tree | |
| trex | Tree Explorer With Multiple Devices | |
| rTraitMult | Multivariate Character Simulation | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| read.tree | Read Tree File in Parenthetic Format | |
| root | Roots Phylogenetic Trees | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| bd.time | Time-Dependent Birth-Death Models | |
| rTraitDisc | Discrete Character Simulation | |
| diversity.contrast.test | Diversity Contrast Test | |
| mst | Minimum Spanning Tree | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| pcoa | Principal Coordinate Analysis | |
| evonet | Evolutionary Networks | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| lmorigin | Multiple regression through the origin | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| yule.cov | Fits the Yule Model With Covariates | |
| compute.brlen | Branch Lengths Computation | |
| phymltest | Fits a Bunch of Models with PhyML | |
| mat5Mrand | Five Independent Trees | |
| parafit | Test of host-parasite coevolution | |
| No Results! | ||
Last month downloads
Details
| Date | 2012-04-05 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2012-04-05 05:08:17 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2012-04-05 05:54:30 |
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