ape v1.7

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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
drop.tip Remove Tips in a Phylogenetic Tree
GC.content Content in GC from DNA Sequences
ltt.plot Lineages Through Time Plot
Correlogram Compute a correlogram
ratogram Ratogram Computed by Nonparametric Rate Smoothing
compar.cheverud Cheverud's Comparative Method
coalescent.intervals Coalescent Intervals
base.freq Base frequencies from DNA Sequences
as.matching Conversion Between Phylo and Matching Objects
branching.times Branching Times of a Phylogenetic Tree
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
ape-internal Internal Ape Functions
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
compute.brlen Branch lengths Computation
dist.phylo Pairwise Distances from a Phylogenetic Tree
balance Balance of a Dichotomous Phylogenetic Tree
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
axisPhylo Axis on Side of Phylogeny
corGrafen Grafen's (1989) Correlation Structure
corMartins Martins's (1997) Correlation Structure
collapsed.intervals Collapsed Coalescent Intervals
node.depth Depth of Nodes and Tips
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
chiroptera Bat Phylogeny
node.leafnumber Get the Number of Leaves for a Node
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
as.phylo Conversion Among Tree Objects
compar.gee Comparative Analysis with GEEs
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
theta.k Population Parameter THETA using Expected Number of Alleles
ace Ancestral Character Estimation
mantel.test Mantel Test for Similarity of Two Matrices
read.tree Read Tree File in Parenthetic Format
skylineplot Drawing Skyline Plot Graphs
Moran.I Moran's I Autocorrelation Index
root Roots Phylogenetic Trees
chronogram Chronogram Computed by Nonparametric Rate Smoothing
dist.taxo Pairwise Distances from a Taxonomic Level
cherry Number of Cherries and Null Models of Trees
all.equal.phylo Global Comparison of two Phylogenies
read.nexus Read Tree File in Nexus Format
corBrownian Brownian Correlation Structure
dist.gene Pairwise Distances from Genetic Data
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
mrca Find Most Recent Common Ancestors Between Pairs
varcomp Compute Variance Component Estimates
nuc.div Nucleotide Diversity
plot.phylo Plot Phylogenies
phymltest Fits a Bunch of Models with PHYML
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
node.sons Get the list of Sons for a Node
bind.tree Binds Trees
seg.sites Find Segregating Sites in DNA Sequences
write.dna Write DNA Sequences in a File
gammaStat Gamma-Statistic of Pybus and Harvey
diversi.gof Tests of Constant Diversification Rates
theta.h Population Parameter THETA using Homozygosity
compar.lynch Lynch's Comparative Method
carnivora Carnivora body sizes and life history traits
woodmouse Cytochrome b Gene Sequences of Woodmice
dist.dna Pairwise Distances from DNA Sequences
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
mst Minimum Spanning Tree
plot.varcomp Plot Variance Components
write.tree Write Tree File in Parenthetic Format
add.scale.bar Add a Scale Bar to a Phylogeny Plot
landplants Gene Tree of 36 Landplant rbcL Sequences
plot.correlogramList Plot several Correlograms
zoom Zoom on a Portion of a Phylogeny
read.GenBank Read DNA Sequences from GenBank via Internet
rotate Rotate an Internal Branch of a Tree
summary.phylo Print Summary of a Phylogeny
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
nodelabels Labelling the Nodes of a Tree
multi2di Collapse and Resolve Multichotomies
howmanytrees Calculate Numbers of Phylogenetic Trees
read.dna Read DNA Sequences in a File
dist.topo Topological Distances Between Two Trees
corClasses Phylogenetic Correlation Structures
opsin Gene Tree of 32 opsin Sequences
skyline Skyline Plot Estimate of Effective Population Size
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
which.edge Identifies Edges of a Tree
write.nexus Write Tree File in Nexus Format
yule.cov Fits the Yule Model With Covariates
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
pic Phylogenetically Independent Contrasts
yule Fits Yule Model to a Phylogenetic Tree
nj Neighbor-Joining Tree Estimation
xenarthra Molecular Phylogeny of Living Xenarthrans
plot.correlogram Plot a Correlogram
is.ultrametric Test if a Tree is Ultrametric
diversi.time Analysis of Diversification with Survival Models
rtree Generates Random Trees
is.binary.tree Test for Binary Tree
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
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Date 2005-09-19
ZipData no
License GPL version 2 or newer
Packaged Mon Sep 19 10:56:36 2005; paradis

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