ape v1.10-2


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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
gammaStat Gamma-Statistic of Pybus and Harvey
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
drop.tip Remove Tips in a Phylogenetic Tree
base.freq Base frequencies from DNA Sequences
bind.tree Binds Trees
Moran.I Moran's I Autocorrelation Index
axisPhylo Axis on Side of Phylogeny
DNAbin Manipulate DNA Sequences in Bit-Level Format
compute.brlen Branch Lengths Computation
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
DNAmodel Defines Models of DNA Evolution
as.matching Conversion Between Phylo and Matching Objects
collapse.singles Collapse Single Nodes
corBrownian Brownian Correlation Structure
as.alignment Conversion Among DNA Sequence Internal Formats
ace Ancestral Character Estimation
coalescent.intervals Coalescent Intervals
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
GC.content Content in GC from DNA Sequences
dist.dna Pairwise Distances from DNA Sequences
corClasses Phylogenetic Correlation Structures
howmanytrees Calculate Numbers of Phylogenetic Trees
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
all.equal.phylo Global Comparison of two Phylogenies
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
carnivora Carnivora body sizes and life history traits
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
compar.gee Comparative Analysis with GEEs
plot.ancestral Plot Ancestral Character Values on a Tree
as.phylo Conversion Among Tree Objects
consensus Concensus Trees
chronopl Molecular Dating With Penalized Likelihood
evolve.phylo Ancestral Character Simulation
Correlogram Compute a correlogram
skylineplot Drawing Skyline Plot Graphs
add.scale.bar Add a Scale Bar to a Phylogeny Plot
cherry Number of Cherries and Null Models of Trees
is.binary.tree Test for Binary Tree
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
data.nex NEXUS Data Example
branching.times Branching Times of a Phylogenetic Tree
compar.cheverud Cheverud's Comparative Method
corMartins Martins's (1997) Correlation Structure
dist.gene Pairwise Distances from Genetic Data
plot.correlogramList Plot several Correlograms
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
balance Balance of a Dichotomous Phylogenetic Tree
mantel.test Mantel Test for Similarity of Two Matrices
plot.correlogram Plot a Correlogram
read.caic Read Tree File in CAIC Format
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
compar.lynch Lynch's Comparative Method
ltt.plot Lineages Through Time Plot
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
ape-internal Internal Ape Functions
xenarthra Molecular Phylogeny of Living Xenarthrans
theta.k Population Parameter THETA using Expected Number of Alleles
is.ultrametric Test if a Tree is Ultrametric
multi2di Collapse and Resolve Multichotomies
chiroptera Bat Phylogeny
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
read.nexus Read Tree File in Nexus Format
dist.topo Topological Distances Between Two Trees
ladderize Ladderize a Tree
mlphylo Estimating Phylogenies by Maximum Likelihood
print.phylo Compact Display of a Phylogeny
read.GenBank Read DNA Sequences from GenBank via Internet
collapsed.intervals Collapsed Coalescent Intervals
theta.h Population Parameter THETA using Homozygosity
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
root Roots Phylogenetic Trees
landplants Gene Tree of 36 Landplant rbcL Sequences
read.tree Read Tree File in Parenthetic Format
chronogram Chronogram Computed by Nonparametric Rate Smoothing
mst Minimum Spanning Tree
summary.phylo Print Summary of a Phylogeny
rtree Generates Random Trees
corGrafen Grafen's (1989) Correlation Structure
read.nexus.data Read Character Data In NEXUS Format
weight.taxo Pairwise Distances from a Taxonomic Level
nj Neighbor-Joining Tree Estimation
seg.sites Find Segregating Sites in DNA Sequences
nuc.div Nucleotide Diversity
diversi.gof Tests of Constant Diversification Rates
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
phymltest Fits a Bunch of Models with PHYML
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
yule Fits Yule Model to a Phylogenetic Tree
read.dna Read DNA Sequences in a File
mrca Find Most Recent Common Ancestors Between Pairs
diversi.time Analysis of Diversification with Survival Models
which.edge Identifies Edges of a Tree
pic Phylogenetically Independent Contrasts
write.tree Write Tree File in Parenthetic Format
skyline Skyline Plot Estimate of Effective Population Size
opsin Gene Tree of 32 opsin Sequences
write.nexus.data Write Character Data In NEXUS Format
yule.cov Fits the Yule Model With Covariates
reorder.phylo Internal Reordering of Trees
write.nexus Write Tree File in Nexus Format
node.depth Depth of Nodes and Tips
sh.test Shimodaira-Hasegawa Test
plot.varcomp Plot Variance Components
ratogram Ratogram Computed by Nonparametric Rate Smoothing
woodmouse Cytochrome b Gene Sequences of Woodmice
varcomp Compute Variance Component Estimates
plot.phylo Plot Phylogenies
write.dna Write DNA Sequences in a File
zoom Zoom on a Portion of a Phylogeny
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Last month downloads


Date 2007-07-05
ZipData no
License GPL version 2 or newer
URL http://pbil.univ-lyon1.fr/R/ape/
Packaged Thu Jul 5 11:09:07 2007; paradis

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