# ape v1.8-3

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, conversion
of APE trees to and from hclust objects and for 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 | |

base.freq | Base frequencies from DNA Sequences | |

compar.gee | Comparative Analysis with GEEs | |

heterozygosity | Heterozygosity at a Locus Using Gene Frequencies | |

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

compute.brlen | Branch lengths Computation | |

ape-internal | Internal Ape Functions | |

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

DNAmodel | Defines Models of DNA Evolution | |

diversi.gof | Tests of Constant Diversification Rates | |

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

boot.phylo | Tree Bipartition and Bootstrapping Phylogenies | |

coalescent.intervals | Coalescent Intervals | |

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

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

corBrownian | Brownian Correlation Structure | |

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

carnivora | Carnivora body sizes and life history traits | |

skylineplot | Drawing Skyline Plot Graphs | |

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

ace | Ancestral Character Estimation | |

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

as.matching | Conversion Between Phylo and Matching Objects | |

mst | Minimum Spanning Tree | |

read.caic | Read Tree File in CAIC Format | |

as.phylo | Conversion Among Tree Objects | |

gammaStat | Gamma-Statistic of Pybus and Harvey | |

plot.correlogram | Plot a Correlogram | |

axisPhylo | Axis on Side of Phylogeny | |

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

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

compar.cheverud | Cheverud's Comparative Method | |

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

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

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

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

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

mrca | Find Most Recent Common Ancestors Between Pairs | |

chiroptera | Bat Phylogeny | |

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

plot.varcomp | Plot Variance Components | |

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

ltt.plot | Lineages Through Time Plot | |

chronopl | Molecular Dating With Penalized Likelihood | |

Correlogram | Compute a correlogram | |

multi2di | Collapse and Resolve Multichotomies | |

dist.dna | Pairwise Distances from DNA Sequences | |

plot.correlogramList | Plot several Correlograms | |

dist.topo | Topological Distances Between Two Trees | |

rtree | Generates Random Trees | |

compar.ou | Ornstein--Uhlenbeck Model for Continuous Characters | |

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

rotate | Rotate an Internal Branch of a Tree | |

theta.h | Population Parameter THETA using Homozygosity | |

yule | Fits Yule Model to a Phylogenetic Tree | |

varcomp | Compute Variance Component Estimates | |

plot.phylo | Plot Phylogenies | |

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

corClasses | Phylogenetic Correlation Structures | |

which.edge | Identifies Edges of a Tree | |

consensus | Concensus Trees | |

chronogram | Chronogram Computed by Nonparametric Rate Smoothing | |

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

nj | Neighbor-Joining Tree Estimation | |

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

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

zoom | Zoom on a Portion of a Phylogeny | |

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

woodmouse | Cytochrome b Gene Sequences of Woodmice | |

skyline | Skyline Plot Estimate of Effective Population Size | |

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

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

dist.gene | Pairwise Distances from Genetic Data | |

as.phylo.formula | Conversion from Taxonomy Variables to Phylogenetic Trees | |

collapsed.intervals | Collapsed Coalescent Intervals | |

landplants | Gene Tree of 36 Landplant rbcL Sequences | |

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

evolve.phylo | Ancestral Character Simulation | |

nuc.div | Nucleotide Diversity | |

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

root | Roots Phylogenetic Trees | |

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

plot.ancestral | Plot Ancestral Character Values on a Tree | |

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

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

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

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

phymltest | Fits a Bunch of Models with PHYML | |

ratogram | Ratogram Computed by Nonparametric Rate Smoothing | |

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

balance | Balance of a Dichotomous Phylogenetic Tree | |

bind.tree | Binds Trees | |

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

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

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

mlphylo | Estimating Phylogenies by Maximum Likelihood | |

opsin | Gene Tree of 32 opsin Sequences | |

xenarthra | Molecular Phylogeny of Living Xenarthrans | |

nodelabels | Labelling the Nodes and the Tips of a Tree | |

pic | Phylogenetically Independent Contrasts | |

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

compar.lynch | Lynch's Comparative Method | |

howmanytrees | Calculate Numbers of Phylogenetic Trees | |

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

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

node.depth | Depth of Nodes and Tips | |

summary.phylo | Print Summary of a Phylogeny | |

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

No Results! |

## Last month downloads

## Details

Date | 2006-06-05 |

ZipData | no |

License | GPL version 2 or newer |

Packaged | Mon Jun 5 11:03:56 2006; paradis |

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, Jim Lemon |

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