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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, conversion of APE trees to and from hclust objects and for 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
base.freq Base frequencies from DNA Sequences
compar.gee Comparative Analysis with GEEs
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
Moran.I Moran's I Autocorrelation Index
compute.brlen Branch lengths Computation
ape-internal Internal Ape Functions
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
DNAmodel Defines Models of DNA Evolution
diversi.gof Tests of Constant Diversification Rates
corGrafen Grafen's (1989) Correlation Structure
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
coalescent.intervals Coalescent Intervals
drop.tip Remove Tips in a Phylogenetic Tree
cherry Number of Cherries and Null Models of Trees
corBrownian Brownian Correlation Structure
is.binary.tree Test for Binary Tree
carnivora Carnivora body sizes and life history traits
skylineplot Drawing Skyline Plot Graphs
corMartins Martins's (1997) Correlation Structure
ace Ancestral Character Estimation
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
as.matching Conversion Between Phylo and Matching Objects
mst Minimum Spanning Tree
read.caic Read Tree File in CAIC Format
as.phylo Conversion Among Tree Objects
gammaStat Gamma-Statistic of Pybus and Harvey
plot.correlogram Plot a Correlogram
axisPhylo Axis on Side of Phylogeny
read.GenBank Read DNA Sequences from GenBank via Internet
write.dna Write DNA Sequences in a File
compar.cheverud Cheverud's Comparative Method
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
branching.times Branching Times of a Phylogenetic Tree
add.scale.bar Add a Scale Bar to a Phylogeny Plot
all.equal.phylo Global Comparison of two Phylogenies
is.ultrametric Test if a Tree is Ultrametric
mrca Find Most Recent Common Ancestors Between Pairs
chiroptera Bat Phylogeny
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
plot.varcomp Plot Variance Components
read.dna Read DNA Sequences in a File
ltt.plot Lineages Through Time Plot
chronopl Molecular Dating With Penalized Likelihood
Correlogram Compute a correlogram
multi2di Collapse and Resolve Multichotomies
dist.dna Pairwise Distances from DNA Sequences
plot.correlogramList Plot several Correlograms
dist.topo Topological Distances Between Two Trees
rtree Generates Random Trees
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
rotate Rotate an Internal Branch of a Tree
theta.h Population Parameter THETA using Homozygosity
yule Fits Yule Model to a Phylogenetic Tree
varcomp Compute Variance Component Estimates
plot.phylo Plot Phylogenies
write.nexus Write Tree File in Nexus Format
corClasses Phylogenetic Correlation Structures
which.edge Identifies Edges of a Tree
consensus Concensus Trees
chronogram Chronogram Computed by Nonparametric Rate Smoothing
diversi.time Analysis of Diversification with Survival Models
nj Neighbor-Joining Tree Estimation
theta.k Population Parameter THETA using Expected Number of Alleles
mantel.test Mantel Test for Similarity of Two Matrices
zoom Zoom on a Portion of a Phylogeny
node.sons Get the list of Sons for a Node
woodmouse Cytochrome b Gene Sequences of Woodmice
skyline Skyline Plot Estimate of Effective Population Size
yule.cov Fits the Yule Model With Covariates
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
dist.gene Pairwise Distances from Genetic Data
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
collapsed.intervals Collapsed Coalescent Intervals
landplants Gene Tree of 36 Landplant rbcL Sequences
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
evolve.phylo Ancestral Character Simulation
nuc.div Nucleotide Diversity
read.tree Read Tree File in Parenthetic Format
root Roots Phylogenetic Trees
node.leafnumber Get the Number of Leaves for a Node
plot.ancestral Plot Ancestral Character Values on a Tree
weight.taxo Pairwise Distances from a Taxonomic Level
write.tree Write Tree File in Parenthetic Format
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
phymltest Fits a Bunch of Models with PHYML
ratogram Ratogram Computed by Nonparametric Rate Smoothing
GC.content Content in GC from DNA Sequences
balance Balance of a Dichotomous Phylogenetic Tree
bind.tree Binds Trees
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
mlphylo Estimating Phylogenies by Maximum Likelihood
opsin Gene Tree of 32 opsin Sequences
xenarthra Molecular Phylogeny of Living Xenarthrans
nodelabels Labelling the Nodes and the Tips of a Tree
pic Phylogenetically Independent Contrasts
read.nexus Read Tree File in Nexus Format
compar.lynch Lynch's Comparative Method
howmanytrees Calculate Numbers of Phylogenetic Trees
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
node.depth Depth of Nodes and Tips
summary.phylo Print Summary of a Phylogeny
seg.sites Find Segregating Sites in DNA Sequences
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Date 2006-06-05
ZipData no
License GPL version 2 or newer
Packaged Mon Jun 5 11:03:56 2006; paradis

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