ape v1.9-3
0
Monthly downloads
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 | Conversion Among Tree Objects | |
| ltt.plot | Lineages Through Time Plot | |
| klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |
| diversi.time | Analysis of Diversification with Survival Models | |
| birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |
| cherry | Number of Cherries and Null Models of Trees | |
| add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |
| read.nexus | Read Tree File in Nexus Format | |
| collapse.singles | Collapse Single Nodes | |
| boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |
| bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |
| cophenetic.phylo | Pairwise Distances from a Phylogenetic Tree | |
| base.freq | Base frequencies from DNA Sequences | |
| nuc.div | Nucleotide Diversity | |
| axisPhylo | Axis on Side of Phylogeny | |
| corClasses | Phylogenetic Correlation Structures | |
| mantel.test | Mantel Test for Similarity of Two Matrices | |
| compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |
| consensus | Concensus Trees | |
| balance | Balance of a Dichotomous Phylogenetic Tree | |
| NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |
| data.nex | NEXUS Data Example | |
| chronopl | Molecular Dating With Penalized Likelihood | |
| mst | Minimum Spanning Tree | |
| branching.times | Branching Times of a Phylogenetic Tree | |
| diversi.gof | Tests of Constant Diversification Rates | |
| plot.ancestral | Plot Ancestral Character Values on a Tree | |
| as.matching | Conversion Between Phylo and Matching Objects | |
| ladderize | Ladderize a Tree | |
| howmanytrees | Calculate Numbers of Phylogenetic Trees | |
| DNAmodel | Defines Models of DNA Evolution | |
| all.equal.phylo | Global Comparison of two Phylogenies | |
| gammaStat | Gamma-Statistic of Pybus and Harvey | |
| Correlogram | Compute a correlogram | |
| compar.lynch | Lynch's Comparative Method | |
| discrete.dist | Taxonomic Level from a Pairwise Distances Matrix | |
| heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |
| plot.correlogram | Plot a Correlogram | |
| is.ultrametric | Test if a Tree is Ultrametric | |
| print.phylo | Compact Display of a Phylogeny | |
| drop.tip | Remove Tips in a Phylogenetic Tree | |
| read.GenBank | Read DNA Sequences from GenBank via Internet | |
| root | Roots Phylogenetic Trees | |
| nj | Neighbor-Joining Tree Estimation | |
| theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |
| read.dna | Read DNA Sequences in a File | |
| sh.test | Shimodaira-Hasegawa Test | |
| weight.taxo | Pairwise Distances from a Taxonomic Level | |
| nodelabels | Labelling the Nodes, Tips, and Edges of a Tree | |
| compar.cheverud | Cheverud's Comparative Method | |
| collapsed.intervals | Collapsed Coalescent Intervals | |
| chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |
| seg.sites | Find Segregating Sites in DNA Sequences | |
| summary.phylo | Print Summary of a Phylogeny | |
| theta.h | Population Parameter THETA using Homozygosity | |
| yule | Fits Yule Model to a Phylogenetic Tree | |
| theta.k | Population Parameter THETA using Expected Number of Alleles | |
| reorder.phylo | Internal Reordering of Trees | |
| ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |
| node.depth | Depth of Nodes and Tips | |
| Moran.I | Moran's I Autocorrelation Index | |
| compute.brlen | Branch Lengths Computation | |
| Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |
| varcomp | Compute Variance Component Estimates | |
| dist.gene | Pairwise Distances from Genetic Data | |
| write.nexus | Write Tree File in Nexus Format | |
| dist.dna | Pairwise Distances from DNA Sequences | |
| phymltest | Fits a Bunch of Models with PHYML | |
| GC.content | Content in GC from DNA Sequences | |
| rtree | Generates Random Trees | |
| bind.tree | Binds Trees | |
| carnivora | Carnivora body sizes and life history traits | |
| coalescent.intervals | Coalescent Intervals | |
| multi2di | Collapse and Resolve Multichotomies | |
| write.nexus.data | Write Character Data In NEXUS Format | |
| compar.gee | Comparative Analysis with GEEs | |
| bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |
| opsin | Gene Tree of 32 opsin Sequences | |
| read.caic | Read Tree File in CAIC Format | |
| woodmouse | Cytochrome b Gene Sequences of Woodmice | |
| mlphylo | Estimating Phylogenies by Maximum Likelihood | |
| write.dna | Write DNA Sequences in a File | |
| write.tree | Write Tree File in Parenthetic Format | |
| which.edge | Identifies Edges of a Tree | |
| xenarthra | Molecular Phylogeny of Living Xenarthrans | |
| ace | Ancestral Character Estimation | |
| chiroptera | Bat Phylogeny | |
| as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |
| corBrownian | Brownian Correlation Structure | |
| hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |
| corGrafen | Grafen's (1989) Correlation Structure | |
| mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |
| pic | Phylogenetically Independent Contrasts | |
| evolve.phylo | Ancestral Character Simulation | |
| dist.topo | Topological Distances Between Two Trees | |
| panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. | |
| ape-internal | Internal Ape Functions | |
| mrca | Find Most Recent Common Ancestors Between Pairs | |
| landplants | Gene Tree of 36 Landplant rbcL Sequences | |
| plot.phylo | Plot Phylogenies | |
| skyline | Skyline Plot Estimate of Effective Population Size | |
| yule.cov | Fits the Yule Model With Covariates | |
| bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |
| read.tree | Read Tree File in Parenthetic Format | |
| plot.correlogramList | Plot several Correlograms | |
| read.nexus.data | Read Character Data In NEXUS Format | |
| vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |
| zoom | Zoom on a Portion of a Phylogeny | |
| skylineplot | Drawing Skyline Plot Graphs | |
| plot.varcomp | Plot Variance Components | |
| corMartins | Martins's (1997) Correlation Structure | |
| is.binary.tree | Test for Binary Tree | |
| No Results! | ||
Last month downloads
Details
| Date | 2007-02-27 |
| ZipData | no |
| License | GPL version 2 or newer |
| Packaged | Tue Feb 27 01:02:05 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 |
Include our badge in your README
[](http://www.rdocumentation.org/packages/ape)