ape v3.0-7
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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 | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| corClasses | Phylogenetic Correlation Structures | |
| as.phylo | Conversion Among Tree and Network Objects | |
| Initialize.corPhyl | Initialize a `corPhyl' Structure Object | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| bind.tree | Binds Trees | |
| ladderize | Ladderize a Tree | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| coalescent.intervals | Coalescent Intervals | |
| correlogram.formula | Phylogenetic Correlogram | |
| Moran.I | Moran's I Autocorrelation Index | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| bd.time | Time-Dependent Birth-Death Models | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| edges | Draw Additional Edges on a Plotted Tree | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| corMartins | Martins's (1997) Correlation Structure | |
| axisPhylo | Axis on Side of Phylogeny | |
| plot.varcomp | Plot Variance Components | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| rTraitMult | Multivariate Character Simulation | |
| alex | Alignment Explorer With Multiple Devices | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| FastME | Tree Estimation Based on the Minimum Evolution Algorithm | |
| compute.brtime | Compute and Set Branching Times | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| compar.cheverud | Cheverud's Comparative Method | |
| BIONJ | Tree Estimation Based on an Improved Version of the NJ Algorithm | |
| read.nexus | Read Tree File in Nexus Format | |
| consensus | Concensus Trees | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| ace | Ancestral Character Estimation | |
| print.phylo | Compact Display of a Phylogeny | |
| varcomp | Compute Variance Component Estimates | |
| is.compatible | Check Compatibility of Splits | |
| rTraitDisc | Discrete Character Simulation | |
| rlineage | Tree Simulation Under the Time-Dependent Birth--Death Models | |
| mat3 | Three Matrices | |
| matexpo | Matrix Exponential | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| data.nex | NEXUS Data Example | |
| ape-internal | Internal Ape Functions | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| additive | Incomplete Distance Matrix Filling | |
| multiphylo | Manipulating Lists of Trees | |
| mat5M3ID | Five Trees | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| del.gaps | Delete Alignment Gaps in DNA Sequences | |
| ltt.plot | Lineages Through Time Plot | |
| as.bitsplits | Conversion Among Split Classes | |
| mat5Mrand | Five Independent Trees | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| chiroptera | Bat Phylogeny | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| is.binary.tree | Test for Binary Tree | |
| read.caic | Read Tree File in CAIC Format | |
| stree | Generates Systematic Regular Trees | |
| rtree | Generates Random Trees | |
| richness.yule.test | Test of Diversification-Shift With the Yule Process | |
| MPR | Most Parsimonious Reconstruction | |
| reorder.phylo | Internal Reordering of Trees | |
| varCompPhylip | Variance Components with Orthonormal Contrasts | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| base.freq | Base frequencies from DNA Sequences | |
| kronoviz | Plot Multiple Chronograms on the Same Scale | |
| image.DNAbin | Plot of DNA Sequence Alignement | |
| treePop | Tree Popping | |
| triangMtd | Tree Reconstruction Based on the Triangles Method | |
| trex | Tree Explorer With Multiple Devices | |
| collapse.singles | Collapse Single Nodes | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| diversity.contrast.test | Diversity Contrast Test | |
| corBlomberg | Blomberg et al.'s Correlation Structure | |
| read.dna | Read DNA Sequences in a File | |
| read.tree | Read Tree File in Parenthetic Format | |
| mvr | Minimum Variance Reduction | |
| clustal | Multiple Sequence Alignment with External Applications | |
| rTraitCont | Continuous Character Simulation | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| corBrownian | Brownian Correlation Structure | |
| summary.phylo | Print Summary of a Phylogeny | |
| rotate | Swapping sister clades | |
| identify.phylo | Graphical Identification of Nodes and Tips | |
| compute.brlen | Branch Lengths Computation | |
| root | Roots Phylogenetic Trees | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| mcconwaysims.test | McConway-Sims Test of Homogeneous Diversification | |
| evonet | Evolutionary Networks | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| compar.lynch | Lynch's Comparative Method | |
| mixedFontLabel | Mixed Font Labels for Plotting | |
| makeLabel | Label Management | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| subtreeplot | Zoom on a Portion of a Phylogeny by Successive Clicks | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| corPagel | Pagel's ``lambda'' Correlation Structure | |
| yule | Fits the Yule Model to a Phylogenetic Tree | |
| ape-package | Analyses of Phylogenetics and Evolution | |
| subtrees | All subtrees of a Phylogenetic Tree | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| vcv | Phylogenetic Variance-covariance or Correlation Matrix | |
| c.phylo | Building Lists of Trees | |
| SDM | Construction of Consensus Distance Matrix With SDM | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| cophyloplot | Plots two phylogenetic trees face to face with links between the tips. | |
| chronoMPL | Molecular Dating With Mean Path Lengths | |
| compar.gee | Comparative Analysis with GEEs | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| skylineplot | Drawing Skyline Plot Graphs | |
| makeNodeLabel | Makes Node Labels | |
| which.edge | Identifies Edges of a Tree | |
| opsin | Gene Tree of 32 opsin Sequences | |
| speciesTree | Species Tree Estimation | |
| weight.taxo | Define Similarity Matrix | |
| dist.gene | Pairwise Distances from Genetic Data | |
| nj | Neighbor-Joining Tree Estimation | |
| write.nexus | Write Tree File in Nexus Format | |
| unique.multiPhylo | Revomes Duplicate Trees | |
| multi2di | Collapse and Resolve Multichotomies | |
| mst | Minimum Spanning Tree | |
| CADM.global | Congruence among distance matrices | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| diversi.time | Analysis of Diversification with Survival Models | |
| dbd | Probability Density Under Birth--Death Models | |
| write.dna | Write DNA Sequences in a File | |
| parafit | Test of host-parasite coevolution | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| chronos | Molecular Dating by Penalised Likelihood and Maximum Likelihood | |
| yule.cov | Fits the Yule Model With Covariates | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| phymltest | Fits a Bunch of Models with PhyML | |
| lmorigin | Multiple regression through the origin | |
| pic.ortho | Phylogenetically Independent Orthonormal Contrasts | |
| plot.phylo | Plot Phylogenies | |
| delta.plot | Delta Plots | |
| dist.topo | Topological Distances Between Two Trees | |
| diversi.gof | Tests of Constant Diversification Rates | |
| plot.correlogram | Plot a Correlogram | |
| zoom | Zoom on a Portion of a Phylogeny | |
| node.depth | Depth and Heights of Nodes and Tips | |
| pic | Phylogenetically Independent Contrasts | |
| yule.time | Fits the Time-Dependent Yule Model | |
| njs | Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ* | |
| where | Find Patterns in DNA Sequences | |
| write.tree | Write Tree File in Parenthetic Format | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| pcoa | Principal Coordinate Analysis | |
| cherry | Number of Cherries and Null Models of Trees | |
| is.monophyletic | Is Group Monophyletic | |
| slowinskiguyer.test | Slowinski-Guyer Test of Homogeneous Diversification | |
| carnivora | Carnivora body sizes and life history traits | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| No Results! | ||
Last month downloads
Details
| Date | 2013-01-19 |
| ZipData | no |
| License | GPL (>= 2) |
| URL | http://ape.mpl.ird.fr/ |
| Packaged | 2013-01-19 11:36:11 UTC; paradis |
| Repository | CRAN |
| Date/Publication | 2013-01-21 14:52:45 |
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