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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.formula Conversion from Taxonomy Variables to Phylogenetic Trees
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
ltt.plot Lineages Through Time Plot
landplants Gene Tree of 36 Landplant rbcL Sequences
collapse.singles Collapse Single Nodes
corClasses Phylogenetic Correlation Structures
corBrownian Brownian Correlation Structure
gammaStat Gamma-Statistic of Pybus and Harvey
multi2di Collapse and Resolve Multichotomies
carnivora Carnivora body sizes and life history traits
write.dna Write DNA Sequences in a File
compar.lynch Lynch's Comparative Method
as.matching Conversion Between Phylo and Matching Objects
chronopl Molecular Dating With Penalized Likelihood
coalescent.intervals Coalescent Intervals
dist.dna Pairwise Distances from DNA Sequences
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
collapsed.intervals Collapsed Coalescent Intervals
dist.gene Pairwise Distances from Genetic Data
mlphylo Estimating Phylogenies by Maximum Likelihood
phymltest Fits a Bunch of Models with PHYML
ladderize Ladderize a Tree
diversi.time Analysis of Diversification with Survival Models
plot.correlogramList Plot several Correlograms
skyline Skyline Plot Estimate of Effective Population Size
read.dna Read DNA Sequences in a File
Moran.I Moran's I Autocorrelation Index
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
ape-internal Internal Ape Functions
axisPhylo Axis on Side of Phylogeny
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
compar.cheverud Cheverud's Comparative Method
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
cherry Number of Cherries and Null Models of Trees
mantel.test Mantel Test for Similarity of Two Matrices
howmanytrees Calculate Numbers of Phylogenetic Trees
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
compute.brlen Branch Lengths Computation
is.binary.tree Test for Binary Tree
nj Neighbor-Joining Tree Estimation
xenarthra Molecular Phylogeny of Living Xenarthrans
yule Fits Yule Model to a Phylogenetic Tree
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
plot.ancestral Plot Ancestral Character Values on a Tree
add.scale.bar Add a Scale Bar to a Phylogeny Plot
read.caic Read Tree File in CAIC Format
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
ratogram Ratogram Computed by Nonparametric Rate Smoothing
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
woodmouse Cytochrome b Gene Sequences of Woodmice
data.nex NEXUS Data Example
ace Ancestral Character Estimation
mrca Find Most Recent Common Ancestors Between Pairs
root Roots Phylogenetic Trees
theta.h Population Parameter THETA using Homozygosity
sh.test Shimodaira-Hasegawa Test
weight.taxo Pairwise Distances from a Taxonomic Level
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
skylineplot Drawing Skyline Plot Graphs
nodelabels Labelling the Nodes and the Tips of a Tree
read.nexus.data Read Character Data In NEXUS Format
nuc.div Nucleotide Diversity
as.phylo Conversion Among Tree Objects
zoom Zoom on a Portion of a Phylogeny
node.depth Depth of Nodes and Tips
rtree Generates Random Trees
Correlogram Compute a correlogram
balance Balance of a Dichotomous Phylogenetic Tree
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
chronogram Chronogram Computed by Nonparametric Rate Smoothing
all.equal.phylo Global Comparison of two Phylogenies
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
write.tree Write Tree File in Parenthetic Format
seg.sites Find Segregating Sites in DNA Sequences
plot.varcomp Plot Variance Components
branching.times Branching Times of a Phylogenetic Tree
plot.correlogram Plot a Correlogram
read.GenBank Read DNA Sequences from GenBank via Internet
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
corMartins Martins's (1997) Correlation Structure
write.nexus.data Write Character Data In NEXUS Format
plot.phylo Plot Phylogenies
pic Phylogenetically Independent Contrasts
summary.phylo Print Summary of a Phylogeny
dist.topo Topological Distances Between Two Trees
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
consensus Concensus Trees
diversi.gof Tests of Constant Diversification Rates
drop.tip Remove Tips in a Phylogenetic Tree
compar.gee Comparative Analysis with GEEs
mst Minimum Spanning Tree
varcomp Compute Variance Component Estimates
opsin Gene Tree of 32 opsin Sequences
bind.tree Binds Trees
base.freq Base frequencies from DNA Sequences
DNAmodel Defines Models of DNA Evolution
chiroptera Bat Phylogeny
read.nexus Read Tree File in Nexus Format
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
evolve.phylo Ancestral Character Simulation
read.tree Read Tree File in Parenthetic Format
print.phylo Compact Display of a Phylogeny
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
GC.content Content in GC from DNA Sequences
is.ultrametric Test if a Tree is Ultrametric
corGrafen Grafen's (1989) Correlation Structure
reorder.phylo Internal Reordering of Trees
which.edge Identifies Edges of a Tree
yule.cov Fits the Yule Model With Covariates
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
write.nexus Write Tree File in Nexus Format
theta.k Population Parameter THETA using Expected Number of Alleles
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Date 2007-01-23
ZipData no
License GPL version 2 or newer
Packaged Tue Jan 23 19:17:48 2007; paradis

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