ape v1.10-2
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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, the population
parameter theta based on various approaches, nucleotide diversity,
generalized skyline plots, estimation of absolute evolutionary rates
and clock-like trees using non-parametric rate smoothing and penalized
likelihood, classifying genes in trees using the Klastorin-Misawa-Tajima
approach. Phylogeny estimation can be done with the NJ and ML methods.
Functions in ape
| Name | Description | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| base.freq | Base frequencies from DNA Sequences | |
| bind.tree | Binds Trees | |
| Moran.I | Moran's I Autocorrelation Index | |
| axisPhylo | Axis on Side of Phylogeny | |
| DNAbin | Manipulate DNA Sequences in Bit-Level Format | |
| compute.brlen | Branch Lengths Computation | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| DNAmodel | Defines Models of DNA Evolution | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| collapse.singles | Collapse Single Nodes | |
| corBrownian | Brownian Correlation Structure | |
| as.alignment | Conversion Among DNA Sequence Internal Formats | |
| ace | Ancestral Character Estimation | |
| coalescent.intervals | Coalescent Intervals | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| GC.content | Content in GC from DNA Sequences | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| corClasses | Phylogenetic Correlation Structures | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| carnivora | Carnivora body sizes and life history traits | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| compar.gee | Comparative Analysis with GEEs | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| as.phylo | Conversion Among Tree Objects | |
| consensus | Concensus Trees | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| evolve.phylo | Ancestral Character Simulation | |
| Correlogram | Compute a correlogram | |
| skylineplot | Drawing Skyline Plot Graphs | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| cherry | Number of Cherries and Null Models of Trees | |
| is.binary.tree | Test for Binary Tree | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| data.nex | NEXUS Data Example | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| compar.cheverud | Cheverud's Comparative Method | |
| corMartins | Martins's (1997) Correlation Structure | |
| dist.gene | Pairwise Distances from Genetic Data | |
| plot.correlogramList | Plot several Correlograms | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| plot.correlogram | Plot a Correlogram | |
| read.caic | Read Tree File in CAIC Format | |
| discrete.dist | Taxonomic Level from a Pairwise Distances Matrix | |
| compar.lynch | Lynch's Comparative Method | |
| ltt.plot | Lineages Through Time Plot | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| ape-internal | Internal Ape Functions | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| multi2di | Collapse and Resolve Multichotomies | |
| chiroptera | Bat Phylogeny | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| read.nexus | Read Tree File in Nexus Format | |
| dist.topo | Topological Distances Between Two Trees | |
| ladderize | Ladderize a Tree | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| print.phylo | Compact Display of a Phylogeny | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| theta.h | Population Parameter THETA using Homozygosity | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| root | Roots Phylogenetic Trees | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| read.tree | Read Tree File in Parenthetic Format | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| mst | Minimum Spanning Tree | |
| summary.phylo | Print Summary of a Phylogeny | |
| rtree | Generates Random Trees | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| weight.taxo | Pairwise Distances from a Taxonomic Level | |
| nj | Neighbor-Joining Tree Estimation | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| nuc.div | Nucleotide Diversity | |
| diversi.gof | Tests of Constant Diversification Rates | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| phymltest | Fits a Bunch of Models with PHYML | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| read.dna | Read DNA Sequences in a File | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| diversi.time | Analysis of Diversification with Survival Models | |
| which.edge | Identifies Edges of a Tree | |
| pic | Phylogenetically Independent Contrasts | |
| write.tree | Write Tree File in Parenthetic Format | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| opsin | Gene Tree of 32 opsin Sequences | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| yule.cov | Fits the Yule Model With Covariates | |
| reorder.phylo | Internal Reordering of Trees | |
| write.nexus | Write Tree File in Nexus Format | |
| node.depth | Depth of Nodes and Tips | |
| sh.test | Shimodaira-Hasegawa Test | |
| plot.varcomp | Plot Variance Components | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| varcomp | Compute Variance Component Estimates | |
| plot.phylo | Plot Phylogenies | |
| write.dna | Write DNA Sequences in a File | |
| zoom | Zoom on a Portion of a Phylogeny | |
| No Results! | ||
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Details
| Date | 2007-07-05 |
| ZipData | no |
| License | GPL version 2 or newer |
| URL | http://pbil.univ-lyon1.fr/R/ape/ |
| Packaged | Thu Jul 5 11:09:07 2007; paradis |
| depends | base (>= 2.0.0) , R (>= 2.0.0) |
| suggests | gee , lattice , nlme |
| Contributors | Emmanuel Paradis, Ben Bolker, Julien Claude, Benoit Durand, Julien Dutheil, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Gangolf Jobb |
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