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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
branching.times Branching Times of a Phylogenetic Tree
dist.gene Pairwise Distances from Genetic Data
dist.topo Topological Distances Between Two Trees
howmanytrees Calculate Numbers of Phylogenetic Trees
collapse.singles Collapse Single Nodes
carnivora Carnivora body sizes and life history traits
plot.ancestral Plot Ancestral Character Values on a Tree
compute.brlen Branch Lengths Computation
nj Neighbor-Joining Tree Estimation
axisPhylo Axis on Side of Phylogeny
balance Balance of a Dichotomous Phylogenetic Tree
all.equal.phylo Global Comparison of two Phylogenies
compar.cheverud Cheverud's Comparative Method
seg.sites Find Segregating Sites in DNA Sequences
Correlogram Compute a correlogram
collapsed.intervals Collapsed Coalescent Intervals
diversi.gof Tests of Constant Diversification Rates
pic Phylogenetically Independent Contrasts
print.phylo Compact Display of a Phylogeny
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
diversi.time Analysis of Diversification with Survival Models
consensus Concensus Trees
ltt.plot Lineages Through Time Plot
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
xenarthra Molecular Phylogeny of Living Xenarthrans
rotate Rotate an Internal Branch of a Tree
Moran.I Moran's I Autocorrelation Index
ace Ancestral Character Estimation
plot.correlogram Plot a Correlogram
read.nexus.data Read Character Data In NEXUS Format
landplants Gene Tree of 36 Landplant rbcL Sequences
as.phylo Conversion Among Tree Objects
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
coalescent.intervals Coalescent Intervals
bind.tree Binds Trees
read.dna Read DNA Sequences in a File
ape-internal Internal Ape Functions
rtree Generates Random Trees
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
read.nexus Read Tree File in Nexus Format
nuc.div Nucleotide Diversity
corMartins Martins's (1997) Correlation Structure
varcomp Compute Variance Component Estimates
reorder.phylo Internal Reordering of Trees
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
read.GenBank Read DNA Sequences from GenBank via Internet
plot.varcomp Plot Variance Components
chiroptera Bat Phylogeny
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
corBrownian Brownian Correlation Structure
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
node.depth Depth of Nodes and Tips
zoom Zoom on a Portion of a Phylogeny
compar.gee Comparative Analysis with GEEs
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
skyline Skyline Plot Estimate of Effective Population Size
corClasses Phylogenetic Correlation Structures
yule Fits Yule Model to a Phylogenetic Tree
write.dna Write DNA Sequences in a File
mrca Find Most Recent Common Ancestors Between Pairs
which.edge Identifies Edges of a Tree
skylineplot Drawing Skyline Plot Graphs
dist.dna Pairwise Distances from DNA Sequences
data.nex NEXUS Data Example
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
drop.tip Remove Tips in a Phylogenetic Tree
read.tree Read Tree File in Parenthetic Format
woodmouse Cytochrome b Gene Sequences of Woodmice
plot.phylo Plot Phylogenies
write.nexus Write Tree File in Nexus Format
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
summary.phylo Print Summary of a Phylogeny
is.ultrametric Test if a Tree is Ultrametric
mst Minimum Spanning Tree
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
mantel.test Mantel Test for Similarity of Two Matrices
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
gammaStat Gamma-Statistic of Pybus and Harvey
is.binary.tree Test for Binary Tree
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
multi2di Collapse and Resolve Multichotomies
evolve.phylo Ancestral Character Simulation
weight.taxo Pairwise Distances from a Taxonomic Level
root Roots Phylogenetic Trees
ratogram Ratogram Computed by Nonparametric Rate Smoothing
theta.h Population Parameter THETA using Homozygosity
yule.cov Fits the Yule Model With Covariates
write.tree Write Tree File in Parenthetic Format
nodelabels Labelling the Nodes and the Tips of a Tree
GC.content Content in GC from DNA Sequences
DNAmodel Defines Models of DNA Evolution
mlphylo Estimating Phylogenies by Maximum Likelihood
theta.k Population Parameter THETA using Expected Number of Alleles
corGrafen Grafen's (1989) Correlation Structure
base.freq Base frequencies from DNA Sequences
chronogram Chronogram Computed by Nonparametric Rate Smoothing
compar.lynch Lynch's Comparative Method
plot.correlogramList Plot several Correlograms
sh.test Shimodaira-Hasegawa Test
add.scale.bar Add a Scale Bar to a Phylogeny Plot
chronopl Molecular Dating With Penalized Likelihood
phymltest Fits a Bunch of Models with PHYML
cherry Number of Cherries and Null Models of Trees
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
read.caic Read Tree File in CAIC Format
as.matching Conversion Between Phylo and Matching Objects
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
opsin Gene Tree of 32 opsin Sequences
write.nexus.data Write Character Data In NEXUS Format
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
ladderize Ladderize a Tree
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Date 2006-12-14
ZipData no
License GPL version 2 or newer
Packaged Thu Dec 14 10:17:58 2006; paradis

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