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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
Correlogram Compute a correlogram
axisPhylo Axis on Side of Phylogeny
dist.gene Pairwise Distances from Genetic Data
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
diversi.time Analysis of Diversification with Survival Models
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
base.freq Base frequencies from DNA Sequences
collapsed.intervals Collapsed Coalescent Intervals
compute.brlen Branch lengths Computation
compar.cheverud Cheverud's Comparative Method
cherry Number of Cherries and Null Models of Trees
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
howmanytrees Calculate Numbers of Phylogenetic Trees
ltt.plot Lineages Through Time Plot
evolve.phylo Ancestral Character Simulation
landplants Gene Tree of 36 Landplant rbcL Sequences
ape-internal Internal Ape Functions
mrca Find Most Recent Common Ancestors Between Pairs
read.dna Read DNA Sequences in a File
read.GenBank Read DNA Sequences from GenBank via Internet
theta.k Population Parameter THETA using Expected Number of Alleles
skyline Skyline Plot Estimate of Effective Population Size
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
zoom Zoom on a Portion of a Phylogeny
all.equal.phylo Global Comparison of two Phylogenies
drop.tip Remove Tips in a Phylogenetic Tree
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
consensus Concensus Trees
read.nexus Read Tree File in Nexus Format
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
node.leafnumber Get the Number of Leaves for a Node
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
plot.phylo Plot Phylogenies
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
corMartins Martins's (1997) Correlation Structure
chronogram Chronogram Computed by Nonparametric Rate Smoothing
weight.taxo Pairwise Distances from a Taxonomic Level
corGrafen Grafen's (1989) Correlation Structure
corBrownian Brownian Correlation Structure
dist.dna Pairwise Distances from DNA Sequences
corClasses Phylogenetic Correlation Structures
rotate Rotate an Internal Branch of a Tree
rtree Generates Random Trees
yule.cov Fits the Yule Model With Covariates
write.dna Write DNA Sequences in a File
read.tree Read Tree File in Parenthetic Format
nuc.div Nucleotide Diversity
plot.varcomp Plot Variance Components
xenarthra Molecular Phylogeny of Living Xenarthrans
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
GC.content Content in GC from DNA Sequences
chronopl Molecular Dating With Penalized Likelihood
chiroptera Bat Phylogeny
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
bind.tree Binds Trees
mst Minimum Spanning Tree
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
node.sons Get the list of Sons for a Node
as.matching Conversion Between Phylo and Matching Objects
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
varcomp Compute Variance Component Estimates
nj Neighbor-Joining Tree Estimation
write.tree Write Tree File in Parenthetic Format
plot.correlogramList Plot several Correlograms
write.nexus Write Tree File in Nexus Format
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
dist.topo Topological Distances Between Two Trees
summary.phylo Print Summary of a Phylogeny
phymltest Fits a Bunch of Models with PHYML
ratogram Ratogram Computed by Nonparametric Rate Smoothing
mantel.test Mantel Test for Similarity of Two Matrices
root Roots Phylogenetic Trees
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
is.binary.tree Test for Binary Tree
pic Phylogenetically Independent Contrasts
coalescent.intervals Coalescent Intervals
nodelabels Labelling the Nodes and the Tips of a Tree
read.caic Read Tree File in CAIC Format
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
plot.correlogram Plot a Correlogram
theta.h Population Parameter THETA using Homozygosity
multi2di Collapse and Resolve Multichotomies
skylineplot Drawing Skyline Plot Graphs
yule Fits Yule Model to a Phylogenetic Tree
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
which.edge Identifies Edges of a Tree
balance Balance of a Dichotomous Phylogenetic Tree
is.ultrametric Test if a Tree is Ultrametric
Moran.I Moran's I Autocorrelation Index
as.phylo Conversion Among Tree Objects
ace Ancestral Character Estimation
carnivora Carnivora body sizes and life history traits
compar.lynch Lynch's Comparative Method
woodmouse Cytochrome b Gene Sequences of Woodmice
diversi.gof Tests of Constant Diversification Rates
mlphylo Estimating Phylogenies by Maximum Likelihood
DNAmodel Defines Models of DNA Evolution
branching.times Branching Times of a Phylogenetic Tree
compar.gee Comparative Analysis with GEEs
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
gammaStat Gamma-Statistic of Pybus and Harvey
node.depth Depth of Nodes and Tips
opsin Gene Tree of 32 opsin Sequences
plot.ancestral Plot Ancestral Character Values on a Tree
seg.sites Find Segregating Sites in DNA Sequences
add.scale.bar Add a Scale Bar to a Phylogeny Plot
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Date 2006-03-24
ZipData no
License GPL version 2 or newer
Packaged Fri Mar 24 03:42:08 2006; paradis

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