ape v1.5
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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, conversion
of APE trees to and from hclust objects and for classifying genes in
trees using the Klastorin-Misawa-Tajima approach.
Functions in ape
| Name | Description | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| cherry | Number of Cherries and Null Models of Trees | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| GC.content | Content in GC from DNA Sequences | |
| ape-internal | Internal Ape Functions | |
| discrete.dist | Taxonomic Level from a Pairwise Distances Matrix | |
| diversi.gof | Tests of Constant Diversification Rates | |
| rtree | Generates Random Trees | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| Correlogram | Compute a correlogram | |
| mst | Minimum Spanning Tree | |
| bind.tree | Binds Trees | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| is.binary.tree | Test for Binary Tree | |
| as.phylo | Conversion Among Tree Objects | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| base.freq | Base frequencies from DNA Sequences | |
| phymltest | Fits a Bunch of Models with PHYML | |
| compar.cheverud | Cheverud's Comparative Method | |
| coalescent.intervals | Coalescent Intervals | |
| corBrownian | Brownian Correlation Structure | |
| read.dna | Read DNA Sequences in a File | |
| axisPhylo | Axis on Side of Phylogeny | |
| panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. | |
| read.tree | Read Tree File in Parenthetic Format | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| dist.gene | Pairwise Distances from Genetic Data | |
| plot.varcomp | Plot Variance Components | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| node.sons | Get the list of Sons for a Node | |
| compar.gee | Comparative Analysis with GEEs | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| compar.lynch | Lynch's Comparative Method | |
| ltt.plot | Lineages Through Time Plot | |
| Moran.I | Moran's I Autocorrelation Index | |
| corMartins | Martins's (1997) Correlation Structure | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| chiroptera | Bat Phylogeny | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| skylineplot | Drawing Skyline Plot Graphs | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| write.dna | Write DNA Sequences in a File | |
| diversi.time | Analysis of Diversification with Survival Models | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| zoom | Zoom on a Portion of a Phylogeny | |
| dist.taxo | Pairwise Distances from a Taxonomic Level | |
| varcomp | Compute Variance Component Estimates | |
| node.leafnumber | Get the Number of Leaves for a Node | |
| compute.brlen | Branch lengths Computation | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| carnivora | Carnivora body sizes and life history traits | |
| nj | Neighbor-Joining Tree Estimation | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| opsin | Gene Tree of 32 opsin Sequences | |
| corClasses | Phylogenetic Correlation Structures | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| which.edge | Identifies Edges of a Tree | |
| write.tree | Write Tree File in Parenthetic Format | |
| node.depth | Depth of Nodes and Tips | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| multi2di | Collapse and Resolve Multichotomies | |
| pic | Phylogenetically Independent Contrasts | |
| dist.phylo | Pairwise Distances from a Phylogenetic Tree | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| theta.h | Population Parameter THETA using Homozygosity | |
| rotate | Rotate an Internal Branch of a Tree | |
| root | Roots Phylogenetic Trees | |
| plot.phylo | Plot Phylogenies | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| read.nexus | Read Tree File in Nexus Format | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| nuc.div | Nucleotide Diversity | |
| plot.correlogramList | Plot several Correlograms | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| nodelabels | Labelling the Nodes of a Tree | |
| summary.phylo | Print Summary of a Phylogeny | |
| plot.correlogram | Plot a Correlogram | |
| write.nexus | Write Tree File in Nexus Format | |
| yule.cov | Fits the Yule Model With Covariates | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| No Results! | ||
Last month downloads
Details
| Date | 2005-04-14 |
| ZipData | no |
| License | GPL version 2 or newer |
| Packaged | Fri Apr 15 20:45:11 2005; root |
| depends | base (>= 2.0.0) , R (>= 2.0.0) |
| suggests | gee , lattice , nlme |
| Contributors | Emmanuel Paradis, Korbinian Strimmer, Julien Claude, Gangolf Jobb, Rainer Opgen-Rhein, Julien Dutheil, Yvonnick Noel, Ben Bolker |
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