ape v1.9-2
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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 | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| ltt.plot | Lineages Through Time Plot | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| collapse.singles | Collapse Single Nodes | |
| corClasses | Phylogenetic Correlation Structures | |
| corBrownian | Brownian Correlation Structure | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| multi2di | Collapse and Resolve Multichotomies | |
| carnivora | Carnivora body sizes and life history traits | |
| write.dna | Write DNA Sequences in a File | |
| compar.lynch | Lynch's Comparative Method | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| coalescent.intervals | Coalescent Intervals | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| dist.gene | Pairwise Distances from Genetic Data | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| phymltest | Fits a Bunch of Models with PHYML | |
| ladderize | Ladderize a Tree | |
| diversi.time | Analysis of Diversification with Survival Models | |
| plot.correlogramList | Plot several Correlograms | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| read.dna | Read DNA Sequences in a File | |
| Moran.I | Moran's I Autocorrelation Index | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| ape-internal | Internal Ape Functions | |
| axisPhylo | Axis on Side of Phylogeny | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| compar.cheverud | Cheverud's Comparative Method | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| cherry | Number of Cherries and Null Models of Trees | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| compute.brlen | Branch Lengths Computation | |
| is.binary.tree | Test for Binary Tree | |
| nj | Neighbor-Joining Tree Estimation | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| read.caic | Read Tree File in CAIC Format | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| data.nex | NEXUS Data Example | |
| ace | Ancestral Character Estimation | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| root | Roots Phylogenetic Trees | |
| theta.h | Population Parameter THETA using Homozygosity | |
| sh.test | Shimodaira-Hasegawa Test | |
| weight.taxo | Pairwise Distances from a Taxonomic Level | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| skylineplot | Drawing Skyline Plot Graphs | |
| nodelabels | Labelling the Nodes and the Tips of a Tree | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| nuc.div | Nucleotide Diversity | |
| as.phylo | Conversion Among Tree Objects | |
| zoom | Zoom on a Portion of a Phylogeny | |
| node.depth | Depth of Nodes and Tips | |
| rtree | Generates Random Trees | |
| Correlogram | Compute a correlogram | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| write.tree | Write Tree File in Parenthetic Format | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| plot.varcomp | Plot Variance Components | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| plot.correlogram | Plot a Correlogram | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| discrete.dist | Taxonomic Level from a Pairwise Distances Matrix | |
| corMartins | Martins's (1997) Correlation Structure | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| plot.phylo | Plot Phylogenies | |
| pic | Phylogenetically Independent Contrasts | |
| summary.phylo | Print Summary of a Phylogeny | |
| dist.topo | Topological Distances Between Two Trees | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| consensus | Concensus Trees | |
| diversi.gof | Tests of Constant Diversification Rates | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| compar.gee | Comparative Analysis with GEEs | |
| mst | Minimum Spanning Tree | |
| varcomp | Compute Variance Component Estimates | |
| opsin | Gene Tree of 32 opsin Sequences | |
| bind.tree | Binds Trees | |
| base.freq | Base frequencies from DNA Sequences | |
| DNAmodel | Defines Models of DNA Evolution | |
| chiroptera | Bat Phylogeny | |
| read.nexus | Read Tree File in Nexus Format | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| evolve.phylo | Ancestral Character Simulation | |
| read.tree | Read Tree File in Parenthetic Format | |
| print.phylo | Compact Display of a Phylogeny | |
| panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. | |
| GC.content | Content in GC from DNA Sequences | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| reorder.phylo | Internal Reordering of Trees | |
| which.edge | Identifies Edges of a Tree | |
| yule.cov | Fits the Yule Model With Covariates | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| write.nexus | Write Tree File in Nexus Format | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| No Results! | ||
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Details
| Date | 2007-01-23 |
| ZipData | no |
| License | GPL version 2 or newer |
| Packaged | Tue Jan 23 19:17:48 2007; paradis |
| depends | base (>= 2.0.0) , R (>= 2.0.0) |
| suggests | gee , lattice , nlme |
| Contributors | Emmanuel Paradis, Ben Bolker, Julien Claude, Julien Dutheil, Jim Lemon, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Gangolf Jobb, Beno�t Durand, Yvonnick No�l |
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