ape v1.6

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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, 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.

Functions in ape

Name Description
axisPhylo Axis on Side of Phylogeny
base.freq Base frequencies from DNA Sequences
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
corMartins Martins's (1997) Correlation Structure
gammaStat Gamma-Statistic of Pybus and Harvey
node.leafnumber Get the Number of Leaves for a Node
opsin Gene Tree of 32 opsin Sequences
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
bind.tree Binds Trees
pic Phylogenetically Independent Contrasts
chronogram Chronogram Computed by Nonparametric Rate Smoothing
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
corClasses Phylogenetic Correlation Structures
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
dist.topo Topological Distances Between Two Trees
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
mantel.test Mantel Test for Similarity of Two Matrices
branching.times Branching Times of a Phylogenetic Tree
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
rtree Generates Random Trees
node.depth Depth of Nodes and Tips
Moran.I Moran's I Autocorrelation Index
nj Neighbor-Joining Tree Estimation
nodelabels Labelling the Nodes of a Tree
Correlogram Compute a correlogram
GC.content Content in GC from DNA Sequences
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
corBrownian Brownian Correlation Structure
diversi.time Analysis of Diversification with Survival Models
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
plot.correlogramList Plot several Correlograms
read.nexus Read Tree File in Nexus Format
woodmouse Cytochrome b Gene Sequences of Woodmice
add.scale.bar Add a Scale Bar to a Phylogeny Plot
write.tree Write Tree File in Parenthetic Format
phymltest Fits a Bunch of Models with PHYML
as.phylo Conversion Among Tree Objects
plot.correlogram Plot a Correlogram
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
node.sons Get the list of Sons for a Node
read.tree Read Tree File in Parenthetic Format
summary.phylo Print Summary of a Phylogeny
read.dna Read DNA Sequences in a File
all.equal.phylo Global Comparison of two Phylogenies
is.ultrametric Test if a Tree is Ultrametric
as.matching Conversion Between Phylo and Matching Objects
howmanytrees Calculate Numbers of Phylogenetic Trees
collapsed.intervals Collapsed Coalescent Intervals
varcomp Compute Variance Component Estimates
yule.cov Fits the Yule Model With Covariates
coalescent.intervals Coalescent Intervals
cherry Number of Cherries and Null Models of Trees
drop.tip Remove Tips in a Phylogenetic Tree
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
dist.gene Pairwise Distances from Genetic Data
carnivora Carnivora body sizes and life history traits
balance Balance of a Dichotomous Phylogenetic Tree
plot.phylo Plot Phylogenies
chiroptera Bat Phylogeny
which.edge Identifies Edges of a Tree
read.GenBank Read DNA Sequences from GenBank via Internet
dist.phylo Pairwise Distances from a Phylogenetic Tree
ape-internal Internal Ape Functions
seg.sites Find Segregating Sites in DNA Sequences
write.nexus Write Tree File in Nexus Format
diversi.gof Tests of Constant Diversification Rates
ratogram Ratogram Computed by Nonparametric Rate Smoothing
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
compute.brlen Branch lengths Computation
compar.lynch Lynch's Comparative Method
skyline Skyline Plot Estimate of Effective Population Size
compar.cheverud Cheverud's Comparative Method
xenarthra Molecular Phylogeny of Living Xenarthrans
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
dist.taxo Pairwise Distances from a Taxonomic Level
root Roots Phylogenetic Trees
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
zoom Zoom on a Portion of a Phylogeny
compar.gee Comparative Analysis with GEEs
ltt.plot Lineages Through Time Plot
corGrafen Grafen's (1989) Correlation Structure
multi2di Collapse and Resolve Multichotomies
dist.dna Pairwise Distances from DNA Sequences
rotate Rotate an Internal Branch of a Tree
nuc.div Nucleotide Diversity
write.dna Write DNA Sequences in a File
mst Minimum Spanning Tree
landplants Gene Tree of 36 Landplant rbcL Sequences
yule Fits Yule Model to a Phylogenetic Tree
is.binary.tree Test for Binary Tree
skylineplot Drawing Skyline Plot Graphs
theta.k Population Parameter THETA using Expected Number of Alleles
plot.varcomp Plot Variance Components
theta.h Population Parameter THETA using Homozygosity
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
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Date 2005-05-31
ZipData no
License GPL version 2 or newer
Packaged Fri Jun 3 10:33:04 2005; paradis

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