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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. Phylogeny estimation can be done with the NJ and ML methods.

Functions in ape

Name Description
base.freq Base frequencies from DNA Sequences
chiroptera Bat Phylogeny
carnivora Carnivora body sizes and life history traits
diversi.time Analysis of Diversification with Survival Models
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
compar.lynch Lynch's Comparative Method
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
diversi.gof Tests of Constant Diversification Rates
corBrownian Brownian Correlation Structure
is.binary.tree Test for Binary Tree
dist.gene Pairwise Distances from Genetic Data
corGrafen Grafen's (1989) Correlation Structure
collapsed.intervals Collapsed Coalescent Intervals
mrca Find Most Recent Common Ancestors Between Pairs
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
chronopl Molecular Dating With Penalized Likelihood
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
plot.correlogram Plot a Correlogram
Correlogram Compute a correlogram
write.nexus Write Tree File in Nexus Format
node.sons Get the list of Sons for a Node
is.ultrametric Test if a Tree is Ultrametric
add.scale.bar Add a Scale Bar to a Phylogeny Plot
write.tree Write Tree File in Parenthetic Format
opsin Gene Tree of 32 opsin Sequences
ratogram Ratogram Computed by Nonparametric Rate Smoothing
yule Fits Yule Model to a Phylogenetic Tree
nuc.div Nucleotide Diversity
multi2di Collapse and Resolve Multichotomies
evolve.phylo Ancestral Character Simulation
zoom Zoom on a Portion of a Phylogeny
rotate Rotate an Internal Branch of a Tree
node.leafnumber Get the Number of Leaves for a Node
as.phylo Conversion Among Tree Objects
mantel.test Mantel Test for Similarity of Two Matrices
cherry Number of Cherries and Null Models of Trees
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
weight.taxo Pairwise Distances from a Taxonomic Level
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
dist.dna Pairwise Distances from DNA Sequences
plot.ancestral Plot Ancestral Character Values on a Tree
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
drop.tip Remove Tips in a Phylogenetic Tree
corClasses Phylogenetic Correlation Structures
read.GenBank Read DNA Sequences from GenBank via Internet
ltt.plot Lineages Through Time Plot
collapse.singles Collapse Single Nodes
branching.times Branching Times of a Phylogenetic Tree
xenarthra Molecular Phylogeny of Living Xenarthrans
seg.sites Find Segregating Sites in DNA Sequences
dist.topo Topological Distances Between Two Trees
howmanytrees Calculate Numbers of Phylogenetic Trees
ape-internal Internal Ape Functions
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
compute.brlen Branch lengths Computation
which.edge Identifies Edges of a Tree
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
corMartins Martins's (1997) Correlation Structure
as.matching Conversion Between Phylo and Matching Objects
read.dna Read DNA Sequences in a File
nj Neighbor-Joining Tree Estimation
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
summary.phylo Print Summary of a Phylogeny
bind.tree Binds Trees
GC.content Content in GC from DNA Sequences
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
theta.h Population Parameter THETA using Homozygosity
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
nodelabels Labelling the Nodes and the Tips of a Tree
plot.phylo Plot Phylogenies
skylineplot Drawing Skyline Plot Graphs
root Roots Phylogenetic Trees
skyline Skyline Plot Estimate of Effective Population Size
landplants Gene Tree of 36 Landplant rbcL Sequences
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
consensus Concensus Trees
coalescent.intervals Coalescent Intervals
DNAmodel Defines Models of DNA Evolution
compar.gee Comparative Analysis with GEEs
gammaStat Gamma-Statistic of Pybus and Harvey
read.nexus Read Tree File in Nexus Format
balance Balance of a Dichotomous Phylogenetic Tree
axisPhylo Axis on Side of Phylogeny
ace Ancestral Character Estimation
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
node.depth Depth of Nodes and Tips
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
woodmouse Cytochrome b Gene Sequences of Woodmice
all.equal.phylo Global Comparison of two Phylogenies
phymltest Fits a Bunch of Models with PHYML
rtree Generates Random Trees
compar.cheverud Cheverud's Comparative Method
plot.varcomp Plot Variance Components
mst Minimum Spanning Tree
read.caic Read Tree File in CAIC Format
varcomp Compute Variance Component Estimates
write.dna Write DNA Sequences in a File
chronogram Chronogram Computed by Nonparametric Rate Smoothing
theta.k Population Parameter THETA using Expected Number of Alleles
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
read.tree Read Tree File in Parenthetic Format
Moran.I Moran's I Autocorrelation Index
plot.correlogramList Plot several Correlograms
pic Phylogenetically Independent Contrasts
sh.test Shimodaira-Hasegawa Test
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
yule.cov Fits the Yule Model With Covariates
mlphylo Estimating Phylogenies by Maximum Likelihood
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Date 2006-07-17
ZipData no
License GPL version 2 or newer
Packaged Mon Jul 17 15:03:03 2006; paradis

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