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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
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Date 2004-11-02
ZipData no
License GPL version 2 or newer
Packaged Wed Nov 10 17:17:55 2004; PARADYS

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