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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
woodmouse Cytochrome b Gene Sequences of Woodmice
mst Minimum Spanning Tree
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
coalescent.intervals Coalescent Intervals
axisPhylo Axis on Side of Phylogeny
corBrownian Brownian Correlation Structure
drop.tip Remove Tips in a Phylogenetic Tree
chronopl Molecular Dating With Penalized Likelihood
Correlogram Compute a correlogram
corGrafen Grafen's (1989) Correlation Structure
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
cherry Number of Cherries and Null Models of Trees
corMartins Martins's (1997) Correlation Structure
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
balance Balance of a Dichotomous Phylogenetic Tree
branching.times Branching Times of a Phylogenetic Tree
ltt.plot Lineages Through Time Plot
plot.varcomp Plot Variance Components
dist.gene Pairwise Distances from Genetic Data
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
all.equal.phylo Global Comparison of two Phylogenies
gammaStat Gamma-Statistic of Pybus and Harvey
compar.lynch Lynch's Comparative Method
skylineplot Drawing Skyline Plot Graphs
opsin Gene Tree of 32 opsin Sequences
data.nex NEXUS Data Example
landplants Gene Tree of 36 Landplant rbcL Sequences
add.scale.bar Add a Scale Bar to a Phylogeny Plot
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
yule.cov Fits the Yule Model With Covariates
read.GenBank Read DNA Sequences from GenBank via Internet
plot.ancestral Plot Ancestral Character Values on a Tree
as.matching Conversion Between Phylo and Matching Objects
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
chronogram Chronogram Computed by Nonparametric Rate Smoothing
GC.content Content in GC from DNA Sequences
theta.k Population Parameter THETA using Expected Number of Alleles
nuc.div Nucleotide Diversity
diversi.gof Tests of Constant Diversification Rates
ape-internal Internal Ape Functions
plot.phylo Plot Phylogenies
ratogram Ratogram Computed by Nonparametric Rate Smoothing
reorder.phylo Internal Reordering of Trees
collapse.singles Collapse Single Nodes
weight.taxo Pairwise Distances from a Taxonomic Level
as.phylo Conversion Among Tree Objects
nj Neighbor-Joining Tree Estimation
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
compute.brlen Branch Lengths Computation
ladderize Ladderize a Tree
Moran.I Moran's I Autocorrelation Index
ace Ancestral Character Estimation
is.binary.tree Test for Binary Tree
yule Fits Yule Model to a Phylogenetic Tree
chiroptera Bat Phylogeny
as.alignment Conversion Among DNA Sequence Internal Formats
read.nexus.data Read Character Data In NEXUS Format
theta.h Population Parameter THETA using Homozygosity
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
rtree Generates Random Trees
read.nexus Read Tree File in Nexus Format
seg.sites Find Segregating Sites in DNA Sequences
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
write.nexus.data Write Character Data In NEXUS Format
write.dna Write DNA Sequences in a File
DNAmodel Defines Models of DNA Evolution
plot.correlogram Plot a Correlogram
mlphylo Estimating Phylogenies by Maximum Likelihood
dist.topo Topological Distances Between Two Trees
collapsed.intervals Collapsed Coalescent Intervals
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
multi2di Collapse and Resolve Multichotomies
dist.dna Pairwise Distances from DNA Sequences
which.edge Identifies Edges of a Tree
zoom Zoom on a Portion of a Phylogeny
write.tree Write Tree File in Parenthetic Format
read.tree Read Tree File in Parenthetic Format
node.depth Depth of Nodes and Tips
mantel.test Mantel Test for Similarity of Two Matrices
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
DNAbin Manipulate DNA Sequences in Bit-Level Format
evolve.phylo Ancestral Character Simulation
base.freq Base frequencies from DNA Sequences
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
bind.tree Binds Trees
howmanytrees Calculate Numbers of Phylogenetic Trees
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
carnivora Carnivora body sizes and life history traits
is.ultrametric Test if a Tree is Ultrametric
diversi.time Analysis of Diversification with Survival Models
pic Phylogenetically Independent Contrasts
skyline Skyline Plot Estimate of Effective Population Size
mrca Find Most Recent Common Ancestors Between Pairs
sh.test Shimodaira-Hasegawa Test
compar.gee Comparative Analysis with GEEs
compar.cheverud Cheverud's Comparative Method
summary.phylo Print Summary of a Phylogeny
phymltest Fits a Bunch of Models with PHYML
consensus Concensus Trees
read.dna Read DNA Sequences in a File
corClasses Phylogenetic Correlation Structures
plot.correlogramList Plot several Correlograms
xenarthra Molecular Phylogeny of Living Xenarthrans
root Roots Phylogenetic Trees
write.nexus Write Tree File in Nexus Format
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
varcomp Compute Variance Component Estimates
read.caic Read Tree File in CAIC Format
print.phylo Compact Display of a Phylogeny
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Date 2007-06-19
ZipData no
License GPL version 2 or newer
URL http://pbil.univ-lyon1.fr/R/ape/
Packaged Tue Jun 19 09:15:45 2007; paradis

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