# ape v1.3-1

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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, 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 | |

node.depth | Depth of Nodes and Tips | |

read.GenBank | Read DNA Sequences from GenBank via Internet | |

mcmc.popsize | Reversible Jump MCMC to Infer Demographic History | |

compar.gee | Comparative Analysis with GEEs | |

diversi.time | Analysis of Diversification with Survival Models | |

heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |

klastorin | Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000) | |

diversi.gof | Tests of Constant Diversification Rates | |

branching.times | Branching Times of a Phylogenetic Tree | |

rtree | Generates Random Trees | |

varcomp | Compute Variance Component Estimates | |

GC.content | Content in GC from DNA Sequences | |

seg.sites | Find Segregating Sites in DNA Sequences | |

read.tree | Read Tree File in Parenthetic Format | |

write.tree | Write Tree File in Parenthetic Format | |

node.sons | Get the list of Sons for a Node | |

dist.phylo | Pairwise Distances from a Phylogenetic Tree | |

bird.families | Phylogeny of the Families of Birds From Sibley and Ahlquist | |

landplants | Gene Tree of 36 Landplant rbcL Sequences | |

chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |

yule.cov | Fits the Yule Model With Covariates | |

gammaStat | Gamma-Statistic of Pybus and Harvey | |

drop.tip | Remove Tips in a Phylogenetic Tree | |

collapsed.intervals | Collapsed Coalescent Intervals | |

corBrownian | Brownian Correlation Structure | |

corGrafen | Grafen's (1989) Correlation Structure | |

base.freq | Base frequencies from DNA Sequences | |

is.ultrametric | Test if a Tree is Ultrametric | |

skyline | Skyline Plot Estimate of Effective Population Size | |

yule | Fits Yule Model to a Phylogenetic Tree | |

coalescent.intervals | Coalescent Intervals | |

compar.lynch | Lynch's Comparative Method | |

read.nexus | Read Tree File in Nexus Format | |

theta.h | Population Parameter THETA using Homozygosity | |

Correlogram | Compute a correlogram | |

mantel.test | Mantel Test for Similarity of Two Matrices | |

plot.correlogramList | Plot several Correlograms | |

theta.s | Population Parameter THETA using Segregating Sites in DNA Sequences | |

phymltest | Fits a Bunch of Models with PHYML | |

write.dna | Write DNA Sequences in a File | |

birthdeath | Estimation of Speciation and Extinction Rates With Birth-Death Models | |

cherry | Number of Cherries and Null Models of Trees | |

all.equal.phylo | Global Comparison of two Phylogenies | |

bind.tree | Binds Trees | |

node.depth.edgelength | Distance from Root to Nodes and Tips | |

compar.cheverud | Cheverud's Comparative Method | |

mst | Minimum Spanning Tree | |

discrete.dist | Taxonomic Level from a Pairwise Distances Matrix | |

dist.dna | Pairwise Distances from DNA Sequences | |

node.leafnumber | Get the Number of Leaves for a Node | |

plot.varcomp | Plot Variance Components | |

ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |

woodmouse | Cytochrome b Gene Sequences of Woodmice | |

Initialize.corPhyl | Initialize a 'corPhyl' Structure Object | |

read.dna | Read DNA Sequences in a File | |

ape-internal | Internal Ape Functions | |

hivtree | Phylogenetic Tree of 193 HIV-1 Sequences | |

NPRS.criterion | Objective Function Employed in Nonparametric Rate Smoothing | |

compute.brlen | Branch lengths Computation | |

ltt.plot | Lineages Through Time Plot | |

add.scale.bar | Add a Scale Bar to a Phylogeny Plot | |

skylineplot | Drawing Skyline Plot Graphs | |

carnivora | Carnivora body sizes and life history traits | |

panel.superpose.correlogram | Lattice panel used in 'plot.correlogramList'. | |

bird.orders | Phylogeny of the Orders of Birds From Sibley and Ahlquist | |

is.binary.tree | Test for Binary Tree | |

plot.phylo | Plot Phylogenies | |

plot.correlogram | Plot a Correlogram | |

root | Roots Phylogenetic Trees | |

write.nexus | Write Tree File in Nexus Format | |

corClasses | Phylogenetic Correlation Structures | |

dist.gene | Pairwise Distances from Genetic Data | |

corMartins | Martins's (1997) Correlation Structure | |

dist.taxo | Pairwise Distances from a Taxonomic Level | |

summary.phylo | Print Summary of a Phylogeny | |

xenarthra | Molecular Phylogeny of Living Xenarthrans | |

zoom | Zoom on a Portion of a Phylogeny | |

Moran.I | Moran's I Autocorrelation Index | |

pic | Phylogenetically Independent Contrasts | |

balance | Balance of a Dichotomous Phylogenetic Tree | |

bd.ext | Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates | |

chiroptera | Bat Phylogeny | |

nodelabels | Labelling the Nodes of a Tree | |

opsin | Gene Tree of 32 opsin Sequences | |

vcv.phylo | Phylogenetic Variance-covariance or Correlation Matrix | |

as.phylo | Conversion between "phylo" and "hclust" trees | |

theta.k | Population Parameter THETA using Expected Number of Alleles | |

rotate | Rotate an Internal Branch of a Tree | |

No Results! |

## Last month downloads

## Details

Date | 2004-11-02 |

ZipData | no |

License | GPL version 2 or newer |

Packaged | Wed Nov 10 17:17:55 2004; PARADYS |

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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