ape v1.9-3

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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 and penalized likelihood, 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
as.phylo Conversion Among Tree Objects
ltt.plot Lineages Through Time Plot
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
diversi.time Analysis of Diversification with Survival Models
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
cherry Number of Cherries and Null Models of Trees
add.scale.bar Add a Scale Bar to a Phylogeny Plot
read.nexus Read Tree File in Nexus Format
collapse.singles Collapse Single Nodes
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
base.freq Base frequencies from DNA Sequences
nuc.div Nucleotide Diversity
axisPhylo Axis on Side of Phylogeny
corClasses Phylogenetic Correlation Structures
mantel.test Mantel Test for Similarity of Two Matrices
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
consensus Concensus Trees
balance Balance of a Dichotomous Phylogenetic Tree
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
data.nex NEXUS Data Example
chronopl Molecular Dating With Penalized Likelihood
mst Minimum Spanning Tree
branching.times Branching Times of a Phylogenetic Tree
diversi.gof Tests of Constant Diversification Rates
plot.ancestral Plot Ancestral Character Values on a Tree
as.matching Conversion Between Phylo and Matching Objects
ladderize Ladderize a Tree
howmanytrees Calculate Numbers of Phylogenetic Trees
DNAmodel Defines Models of DNA Evolution
all.equal.phylo Global Comparison of two Phylogenies
gammaStat Gamma-Statistic of Pybus and Harvey
Correlogram Compute a correlogram
compar.lynch Lynch's Comparative Method
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
plot.correlogram Plot a Correlogram
is.ultrametric Test if a Tree is Ultrametric
print.phylo Compact Display of a Phylogeny
drop.tip Remove Tips in a Phylogenetic Tree
read.GenBank Read DNA Sequences from GenBank via Internet
root Roots Phylogenetic Trees
nj Neighbor-Joining Tree Estimation
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
read.dna Read DNA Sequences in a File
sh.test Shimodaira-Hasegawa Test
weight.taxo Pairwise Distances from a Taxonomic Level
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
compar.cheverud Cheverud's Comparative Method
collapsed.intervals Collapsed Coalescent Intervals
chronogram Chronogram Computed by Nonparametric Rate Smoothing
seg.sites Find Segregating Sites in DNA Sequences
summary.phylo Print Summary of a Phylogeny
theta.h Population Parameter THETA using Homozygosity
yule Fits Yule Model to a Phylogenetic Tree
theta.k Population Parameter THETA using Expected Number of Alleles
reorder.phylo Internal Reordering of Trees
ratogram Ratogram Computed by Nonparametric Rate Smoothing
node.depth Depth of Nodes and Tips
Moran.I Moran's I Autocorrelation Index
compute.brlen Branch Lengths Computation
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
varcomp Compute Variance Component Estimates
dist.gene Pairwise Distances from Genetic Data
write.nexus Write Tree File in Nexus Format
dist.dna Pairwise Distances from DNA Sequences
phymltest Fits a Bunch of Models with PHYML
GC.content Content in GC from DNA Sequences
rtree Generates Random Trees
bind.tree Binds Trees
carnivora Carnivora body sizes and life history traits
coalescent.intervals Coalescent Intervals
multi2di Collapse and Resolve Multichotomies
write.nexus.data Write Character Data In NEXUS Format
compar.gee Comparative Analysis with GEEs
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
opsin Gene Tree of 32 opsin Sequences
read.caic Read Tree File in CAIC Format
woodmouse Cytochrome b Gene Sequences of Woodmice
mlphylo Estimating Phylogenies by Maximum Likelihood
write.dna Write DNA Sequences in a File
write.tree Write Tree File in Parenthetic Format
which.edge Identifies Edges of a Tree
xenarthra Molecular Phylogeny of Living Xenarthrans
ace Ancestral Character Estimation
chiroptera Bat Phylogeny
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
corBrownian Brownian Correlation Structure
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
corGrafen Grafen's (1989) Correlation Structure
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
pic Phylogenetically Independent Contrasts
evolve.phylo Ancestral Character Simulation
dist.topo Topological Distances Between Two Trees
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
ape-internal Internal Ape Functions
mrca Find Most Recent Common Ancestors Between Pairs
landplants Gene Tree of 36 Landplant rbcL Sequences
plot.phylo Plot Phylogenies
skyline Skyline Plot Estimate of Effective Population Size
yule.cov Fits the Yule Model With Covariates
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
read.tree Read Tree File in Parenthetic Format
plot.correlogramList Plot several Correlograms
read.nexus.data Read Character Data In NEXUS Format
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
zoom Zoom on a Portion of a Phylogeny
skylineplot Drawing Skyline Plot Graphs
plot.varcomp Plot Variance Components
corMartins Martins's (1997) Correlation Structure
is.binary.tree Test for Binary Tree
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Date 2007-02-27
ZipData no
License GPL version 2 or newer
Packaged Tue Feb 27 01:02:05 2007; paradis

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