ape v1.9-1
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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 | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| dist.gene | Pairwise Distances from Genetic Data | |
| dist.topo | Topological Distances Between Two Trees | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| collapse.singles | Collapse Single Nodes | |
| carnivora | Carnivora body sizes and life history traits | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| compute.brlen | Branch Lengths Computation | |
| nj | Neighbor-Joining Tree Estimation | |
| axisPhylo | Axis on Side of Phylogeny | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| compar.cheverud | Cheverud's Comparative Method | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| Correlogram | Compute a correlogram | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| diversi.gof | Tests of Constant Diversification Rates | |
| pic | Phylogenetically Independent Contrasts | |
| print.phylo | Compact Display of a Phylogeny | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| diversi.time | Analysis of Diversification with Survival Models | |
| consensus | Concensus Trees | |
| ltt.plot | Lineages Through Time Plot | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| rotate | Rotate an Internal Branch of a Tree | |
| Moran.I | Moran's I Autocorrelation Index | |
| ace | Ancestral Character Estimation | |
| plot.correlogram | Plot a Correlogram | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| as.phylo | Conversion Among Tree Objects | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| coalescent.intervals | Coalescent Intervals | |
| bind.tree | Binds Trees | |
| read.dna | Read DNA Sequences in a File | |
| ape-internal | Internal Ape Functions | |
| rtree | Generates Random Trees | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| read.nexus | Read Tree File in Nexus Format | |
| nuc.div | Nucleotide Diversity | |
| corMartins | Martins's (1997) Correlation Structure | |
| varcomp | Compute Variance Component Estimates | |
| reorder.phylo | Internal Reordering of Trees | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| plot.varcomp | Plot Variance Components | |
| chiroptera | Bat Phylogeny | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| corBrownian | Brownian Correlation Structure | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| node.depth | Depth of Nodes and Tips | |
| zoom | Zoom on a Portion of a Phylogeny | |
| compar.gee | Comparative Analysis with GEEs | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| corClasses | Phylogenetic Correlation Structures | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| write.dna | Write DNA Sequences in a File | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| which.edge | Identifies Edges of a Tree | |
| skylineplot | Drawing Skyline Plot Graphs | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| data.nex | NEXUS Data Example | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| read.tree | Read Tree File in Parenthetic Format | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| plot.phylo | Plot Phylogenies | |
| write.nexus | Write Tree File in Nexus Format | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| summary.phylo | Print Summary of a Phylogeny | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| mst | Minimum Spanning Tree | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| is.binary.tree | Test for Binary Tree | |
| panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. | |
| multi2di | Collapse and Resolve Multichotomies | |
| evolve.phylo | Ancestral Character Simulation | |
| weight.taxo | Pairwise Distances from a Taxonomic Level | |
| root | Roots Phylogenetic Trees | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| theta.h | Population Parameter THETA using Homozygosity | |
| yule.cov | Fits the Yule Model With Covariates | |
| write.tree | Write Tree File in Parenthetic Format | |
| nodelabels | Labelling the Nodes and the Tips of a Tree | |
| GC.content | Content in GC from DNA Sequences | |
| DNAmodel | Defines Models of DNA Evolution | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| base.freq | Base frequencies from DNA Sequences | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| compar.lynch | Lynch's Comparative Method | |
| plot.correlogramList | Plot several Correlograms | |
| sh.test | Shimodaira-Hasegawa Test | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| phymltest | Fits a Bunch of Models with PHYML | |
| cherry | Number of Cherries and Null Models of Trees | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| read.caic | Read Tree File in CAIC Format | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| discrete.dist | Taxonomic Level from a Pairwise Distances Matrix | |
| opsin | Gene Tree of 32 opsin Sequences | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| ladderize | Ladderize a Tree | |
| No Results! | ||
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Details
| Date | 2006-12-14 |
| ZipData | no |
| License | GPL version 2 or newer |
| Packaged | Thu Dec 14 10:17:58 2006; 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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