ape v1.4


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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
chronogram Chronogram Computed by Nonparametric Rate Smoothing
which.edge Identifies Edges of a Tree
ltt.plot Lineages Through Time Plot
base.freq Base frequencies from DNA Sequences
theta.k Population Parameter THETA using Expected Number of Alleles
bind.tree Binds Trees
read.GenBank Read DNA Sequences from GenBank via Internet
coalescent.intervals Coalescent Intervals
corBrownian Brownian Correlation Structure
zoom Zoom on a Portion of a Phylogeny
is.binary.tree Test for Binary Tree
summary.phylo Print Summary of a Phylogeny
mantel.test Mantel Test for Similarity of Two Matrices
diversi.gof Tests of Constant Diversification Rates
Moran.I Moran's I Autocorrelation Index
node.leafnumber Get the Number of Leaves for a Node
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
ratogram Ratogram Computed by Nonparametric Rate Smoothing
node.sons Get the list of Sons for a Node
write.nexus Write Tree File in Nexus Format
read.dna Read DNA Sequences in a File
rotate Rotate an Internal Branch of a Tree
Correlogram Compute a correlogram
mst Minimum Spanning Tree
as.phylo Conversion Among Tree Objects
seg.sites Find Segregating Sites in DNA Sequences
compar.cheverud Cheverud's Comparative Method
plot.correlogram Plot a Correlogram
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
compute.brlen Branch lengths Computation
dist.taxo Pairwise Distances from a Taxonomic Level
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
howmanytrees Calculate Numbers of Phylogenetic Trees
varcomp Compute Variance Component Estimates
add.scale.bar Add a Scale Bar to a Phylogeny Plot
corGrafen Grafen's (1989) Correlation Structure
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
is.ultrametric Test if a Tree is Ultrametric
landplants Gene Tree of 36 Landplant rbcL Sequences
plot.varcomp Plot Variance Components
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
axisPhylo Axis on Side of Phylogeny
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
opsin Gene Tree of 32 opsin Sequences
nodelabels Labelling the Nodes of a Tree
skyline Skyline Plot Estimate of Effective Population Size
yule.cov Fits the Yule Model With Covariates
root Roots Phylogenetic Trees
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
branching.times Branching Times of a Phylogenetic Tree
dist.gene Pairwise Distances from Genetic Data
read.nexus Read Tree File in Nexus Format
yule Fits Yule Model to a Phylogenetic Tree
ape-internal Internal Ape Functions
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
carnivora Carnivora body sizes and life history traits
pic Phylogenetically Independent Contrasts
balance Balance of a Dichotomous Phylogenetic Tree
write.dna Write DNA Sequences in a File
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
corMartins Martins's (1997) Correlation Structure
compar.gee Comparative Analysis with GEEs
read.tree Read Tree File in Parenthetic Format
phymltest Fits a Bunch of Models with PHYML
node.depth Depth of Nodes and Tips
xenarthra Molecular Phylogeny of Living Xenarthrans
skylineplot Drawing Skyline Plot Graphs
write.tree Write Tree File in Parenthetic Format
dist.phylo Pairwise Distances from a Phylogenetic Tree
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
gammaStat Gamma-Statistic of Pybus and Harvey
cherry Number of Cherries and Null Models of Trees
drop.tip Remove Tips in a Phylogenetic Tree
all.equal.phylo Global Comparison of two Phylogenies
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
rtree Generates Random Trees
chiroptera Bat Phylogeny
compar.lynch Lynch's Comparative Method
corClasses Phylogenetic Correlation Structures
nj Neighbor-Joining Tree Estimation
diversi.time Analysis of Diversification with Survival Models
theta.h Population Parameter THETA using Homozygosity
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
dist.dna Pairwise Distances from DNA Sequences
collapsed.intervals Collapsed Coalescent Intervals
plot.correlogramList Plot several Correlograms
woodmouse Cytochrome b Gene Sequences of Woodmice
GC.content Content in GC from DNA Sequences
plot.phylo Plot Phylogenies
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Last month downloads


Date 2004-12-20
ZipData no
License GPL version 2 or newer
Packaged Thu Dec 23 16:08:33 2004; PARADYS

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