ape v1.9-4

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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, 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
landplants Gene Tree of 36 Landplant rbcL Sequences
mantel.test Mantel Test for Similarity of Two Matrices
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
GC.content Content in GC from DNA Sequences
ape-internal Internal Ape Functions
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
ltt.plot Lineages Through Time Plot
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
collapsed.intervals Collapsed Coalescent Intervals
rtree Generates Random Trees
axisPhylo Axis on Side of Phylogeny
gammaStat Gamma-Statistic of Pybus and Harvey
corMartins Martins's (1997) Correlation Structure
carnivora Carnivora body sizes and life history traits
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
chronogram Chronogram Computed by Nonparametric Rate Smoothing
compar.gee Comparative Analysis with GEEs
coalescent.intervals Coalescent Intervals
compute.brlen Branch Lengths Computation
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
theta.k Population Parameter THETA using Expected Number of Alleles
read.tree Read Tree File in Parenthetic Format
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
multi2di Collapse and Resolve Multichotomies
which.edge Identifies Edges of a Tree
root Roots Phylogenetic Trees
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
diversi.gof Tests of Constant Diversification Rates
mst Minimum Spanning Tree
dist.dna Pairwise Distances from DNA Sequences
corBrownian Brownian Correlation Structure
read.GenBank Read DNA Sequences from GenBank via Internet
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
dist.topo Topological Distances Between Two Trees
reorder.phylo Internal Reordering of Trees
Correlogram Compute a correlogram
opsin Gene Tree of 32 opsin Sequences
Moran.I Moran's I Autocorrelation Index
skylineplot Drawing Skyline Plot Graphs
xenarthra Molecular Phylogeny of Living Xenarthrans
theta.h Population Parameter THETA using Homozygosity
consensus Concensus Trees
yule.cov Fits the Yule Model With Covariates
write.dna Write DNA Sequences in a File
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
mlphylo Estimating Phylogenies by Maximum Likelihood
chronopl Molecular Dating With Penalized Likelihood
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
dist.gene Pairwise Distances from Genetic Data
sh.test Shimodaira-Hasegawa Test
is.binary.tree Test for Binary Tree
pic Phylogenetically Independent Contrasts
phymltest Fits a Bunch of Models with PHYML
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
as.phylo Conversion Among Tree Objects
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
bind.tree Binds Trees
ratogram Ratogram Computed by Nonparametric Rate Smoothing
read.dna Read DNA Sequences in a File
varcomp Compute Variance Component Estimates
seg.sites Find Segregating Sites in DNA Sequences
read.caic Read Tree File in CAIC Format
write.nexus Write Tree File in Nexus Format
plot.correlogram Plot a Correlogram
yule Fits Yule Model to a Phylogenetic Tree
compar.lynch Lynch's Comparative Method
howmanytrees Calculate Numbers of Phylogenetic Trees
nj Neighbor-Joining Tree Estimation
is.ultrametric Test if a Tree is Ultrametric
base.freq Base frequencies from DNA Sequences
drop.tip Remove Tips in a Phylogenetic Tree
data.nex NEXUS Data Example
evolve.phylo Ancestral Character Simulation
add.scale.bar Add a Scale Bar to a Phylogeny Plot
balance Balance of a Dichotomous Phylogenetic Tree
ace Ancestral Character Estimation
as.matching Conversion Between Phylo and Matching Objects
branching.times Branching Times of a Phylogenetic Tree
all.equal.phylo Global Comparison of two Phylogenies
chiroptera Bat Phylogeny
cherry Number of Cherries and Null Models of Trees
plot.correlogramList Plot several Correlograms
collapse.singles Collapse Single Nodes
mrca Find Most Recent Common Ancestors Between Pairs
nuc.div Nucleotide Diversity
skyline Skyline Plot Estimate of Effective Population Size
corGrafen Grafen's (1989) Correlation Structure
corClasses Phylogenetic Correlation Structures
write.tree Write Tree File in Parenthetic Format
plot.varcomp Plot Variance Components
summary.phylo Print Summary of a Phylogeny
diversi.time Analysis of Diversification with Survival Models
DNAmodel Defines Models of DNA Evolution
node.depth Depth of Nodes and Tips
read.nexus.data Read Character Data In NEXUS Format
ladderize Ladderize a Tree
compar.cheverud Cheverud's Comparative Method
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
plot.phylo Plot Phylogenies
plot.ancestral Plot Ancestral Character Values on a Tree
print.phylo Compact Display of a Phylogeny
weight.taxo Pairwise Distances from a Taxonomic Level
read.nexus Read Tree File in Nexus Format
woodmouse Cytochrome b Gene Sequences of Woodmice
write.nexus.data Write Character Data In NEXUS Format
zoom Zoom on a Portion of a Phylogeny
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Date 2007-03-27
ZipData no
License GPL version 2 or newer
Packaged Tue Mar 27 10:33:25 2007; paradis

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