ape v1.2-1

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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
dist.gene Pairwise Distances from Genetic Data
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
compar.lynch Lynch's Comparative Method
mst Minimum Spanning Tree
mantel.test Mantel Test for Similarity of Two Matrices
bind.tree Binds Trees
balance Balance of a Dichotomous Phylogenetic Tree
cherry Number of Cherries and Null Models of Trees
xenarthra Molecular Phylogeny of Living Xenarthrans
GC.content Content in GC from DNA Sequences
is.binary.tree Test for Binary Tree
base.freq Base frequencies from DNA Sequences
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
landplants Gene Tree of 36 Landplant rbcL Sequences
read.tree Read Tree File in Parenthetic Format
zoom Zoom on a Portion of a Phylogeny
compar.gee Comparative Analysis with GEEs
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
node.depth.edgelength Distance from Root to Nodes and Tips
chronogram Chronogram Computed by Nonparametric Rate Smoothing
pic Phylogenetically Independent Contrasts
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
plot.phylo Plot Phylogenies
collapsed.intervals Collapsed Coalescent Intervals
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
coalescent.intervals Coalescent Intervals
gammaStat Gamma-Statistic of Pybus and Harvey
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
ape-internal Internal Ape Functions
drop.tip Remove Tips in a Phylogenetic Tree
dist.dna Pairwise Distances from DNA Sequences
chiroptera Bat Phylogeny
diversi.time Analysis of Diversification with Survival Models
node.depth Depth of Nodes and Tips
theta.k Population Parameter THETA using Expected Number of Alleles
skylineplot Drawing Skyline Plot Graphs
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
add.scale.bar Add a Scale Bar to a Phylogeny Plot
diversi.gof Tests of Constant Diversification Rates
ratogram Ratogram Computed by Nonparametric Rate Smoothing
yule Fits Yule Model to a Phylogenetic Tree
write.dna Write DNA Sequences in a File
read.GenBank Read DNA Sequences from GenBank via Internet
read.dna Read DNA Sequences in a File
all.equal.phylo Global Comparison of two Phylogenies
theta.h Population Parameter THETA using Homozygosity
read.nexus Read Tree File in Nexus Format
woodmouse Cytochrome b Sequences of Woodmice
write.nexus Write Tree File in Nexus Format
dist.phylo Pairwise Distances from a Phylogenetic Tree
skyline Skyline Plot Estimate of Effective Population Size
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
write.tree Write Tree File in Parenthetic Format
summary.phylo Print Summary of a Phylogeny
is.ultrametric Test if a Tree is Ultrametric
branching.times Branching Times of a Phylogenetic Tree
as.phylo Conversion between "phylo" and "hclust" trees
opsin Gene Tree of 32 opsin Sequences
ltt.plot Lineages Through Time Plot
seg.sites Find Segregating Sites in DNA Sequences
Moran.I Moran's I Autocorrelation Index
rtree Generates Random Trees
popsize Reversible Jump MCMC to Infer Demographic History
dist.taxo Pairwise Distances from a Taxonomic Level
Correlogram Compute a correlogram
carnivora Carnivora body sizes and life history traits
root Roots Phylogenetic Trees
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
plot.correlogram Plot a Correlogram
rotate Rotate an Internal Branch of a Tree
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Details

Date 2004-02-04
License GPL version 2 or newer
depends gee
Contributors Emmanuel Paradis

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