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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.

Functions in ape

Name Description
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
dist.topo Topological Distances Between Two Trees
as.phylo Conversion Among Tree Objects
all.equal.phylo Global Comparison of two Phylogenies
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
mrca Find Most Recent Common Ancestors Between Pairs
compar.gee Comparative Analysis with GEEs
gammaStat Gamma-Statistic of Pybus and Harvey
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
read.GenBank Read DNA Sequences from GenBank via Internet
chiroptera Bat Phylogeny
diversi.gof Tests of Constant Diversification Rates
pic Phylogenetically Independent Contrasts
compar.cheverud Cheverud's Comparative Method
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
howmanytrees Calculate Numbers of Phylogenetic Trees
collapsed.intervals Collapsed Coalescent Intervals
chronopl Molecular Dating With Penalized Likelihood
diversi.time Analysis of Diversification with Survival Models
compute.brlen Branch lengths Computation
ratogram Ratogram Computed by Nonparametric Rate Smoothing
chronogram Chronogram Computed by Nonparametric Rate Smoothing
drop.tip Remove Tips in a Phylogenetic Tree
read.caic Read Tree File in CAIC Format
ltt.plot Lineages Through Time Plot
corGrafen Grafen's (1989) Correlation Structure
nj Neighbor-Joining Tree Estimation
GC.content Content in GC from DNA Sequences
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
weight.taxo Pairwise Distances from a Taxonomic Level
dist.gene Pairwise Distances from Genetic Data
add.scale.bar Add a Scale Bar to a Phylogeny Plot
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
bind.tree Binds Trees
phymltest Fits a Bunch of Models with PHYML
nuc.div Nucleotide Diversity
rotate Rotate an Internal Branch of a Tree
summary.phylo Print Summary of a Phylogeny
evolve.phylo Ancestral Character Simulation
write.dna Write DNA Sequences in a File
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
plot.varcomp Plot Variance Components
corMartins Martins's (1997) Correlation Structure
Correlogram Compute a correlogram
balance Balance of a Dichotomous Phylogenetic Tree
as.matching Conversion Between Phylo and Matching Objects
xenarthra Molecular Phylogeny of Living Xenarthrans
write.tree Write Tree File in Parenthetic Format
plot.correlogram Plot a Correlogram
multi2di Collapse and Resolve Multichotomies
mantel.test Mantel Test for Similarity of Two Matrices
plot.ancestral Plot Ancestral Character Values on a Tree
axisPhylo Axis on Side of Phylogeny
ace Ancestral Character Estimation
branching.times Branching Times of a Phylogenetic Tree
read.dna Read DNA Sequences in a File
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
base.freq Base frequencies from DNA Sequences
yule Fits Yule Model to a Phylogenetic Tree
carnivora Carnivora body sizes and life history traits
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
theta.h Population Parameter THETA using Homozygosity
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
corBrownian Brownian Correlation Structure
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
landplants Gene Tree of 36 Landplant rbcL Sequences
coalescent.intervals Coalescent Intervals
theta.k Population Parameter THETA using Expected Number of Alleles
woodmouse Cytochrome b Gene Sequences of Woodmice
seg.sites Find Segregating Sites in DNA Sequences
corClasses Phylogenetic Correlation Structures
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
which.edge Identifies Edges of a Tree
skylineplot Drawing Skyline Plot Graphs
compar.lynch Lynch's Comparative Method
Moran.I Moran's I Autocorrelation Index
ape-internal Internal Ape Functions
node.depth Depth of Nodes and Tips
yule.cov Fits the Yule Model With Covariates
cherry Number of Cherries and Null Models of Trees
plot.correlogramList Plot several Correlograms
consensus Concensus Trees
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
read.nexus Read Tree File in Nexus Format
write.nexus Write Tree File in Nexus Format
rtree Generates Random Trees
dist.dna Pairwise Distances from DNA Sequences
opsin Gene Tree of 32 opsin Sequences
varcomp Compute Variance Component Estimates
node.leafnumber Get the Number of Leaves for a Node
is.ultrametric Test if a Tree is Ultrametric
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
read.tree Read Tree File in Parenthetic Format
nodelabels Labelling the Nodes and the Tips of a Tree
node.sons Get the list of Sons for a Node
is.binary.tree Test for Binary Tree
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
mst Minimum Spanning Tree
plot.phylo Plot Phylogenies
root Roots Phylogenetic Trees
skyline Skyline Plot Estimate of Effective Population Size
zoom Zoom on a Portion of a Phylogeny
DNAmodel Defines Models of DNA Evolution
mlphylo Estimating Phylogenies by Maximum Likelihood
collapse.singles Collapse Single Nodes
reorder.phylo Internal Reordering of Trees
sh.test Shimodaira-Hasegawa Test
write.nexus.data Write Character Data In NEXUS Format
data.nex NEXUS Data Example
read.nexus.data Read Character Data In NEXUS Format
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Date 2006-02-17
ZipData no
License GPL version 2 or newer
Packaged Fri Feb 17 17:30:18 2006; hornik

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