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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
Moran.I Moran's I Autocorrelation Index
plot.ancestral Plot Ancestral Character Values on a Tree
corMartins Martins's (1997) Correlation Structure
cherry Number of Cherries and Null Models of Trees
add.scale.bar Add a Scale Bar to a Phylogeny Plot
corGrafen Grafen's (1989) Correlation Structure
collapsed.intervals Collapsed Coalescent Intervals
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
collapse.singles Collapse Single Nodes
node.depth Depth of Nodes and Tips
chiroptera Bat Phylogeny
read.caic Read Tree File in CAIC Format
chronopl Molecular Dating With Penalized Likelihood
data.nex NEXUS Data Example
is.binary.tree Test for Binary Tree
pic Phylogenetically Independent Contrasts
mlphylo Estimating Phylogenies by Maximum Likelihood
compar.cheverud Cheverud's Comparative Method
compar.lynch Lynch's Comparative Method
all.equal.phylo Global Comparison of two Phylogenies
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
zoom Zoom on a Portion of a Phylogeny
theta.h Population Parameter THETA using Homozygosity
ace Ancestral Character Estimation
DNAmodel Defines Models of DNA Evolution
GC.content Content in GC from DNA Sequences
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
node.leafnumber Get the Number of Leaves for a Node
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
mantel.test Mantel Test for Similarity of Two Matrices
compar.gee Comparative Analysis with GEEs
evolve.phylo Ancestral Character Simulation
ape-internal Internal Ape Functions
dist.gene Pairwise Distances from Genetic Data
yule Fits Yule Model to a Phylogenetic Tree
axisPhylo Axis on Side of Phylogeny
weight.taxo Pairwise Distances from a Taxonomic Level
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
read.dna Read DNA Sequences in a File
as.phylo Conversion Among Tree Objects
carnivora Carnivora body sizes and life history traits
base.freq Base frequencies from DNA Sequences
diversi.time Analysis of Diversification with Survival Models
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
compute.brlen Branch lengths Computation
drop.tip Remove Tips in a Phylogenetic Tree
phymltest Fits a Bunch of Models with PHYML
bind.tree Binds Trees
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
Correlogram Compute a correlogram
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
plot.phylo Plot Phylogenies
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
as.matching Conversion Between Phylo and Matching Objects
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
dist.dna Pairwise Distances from DNA Sequences
read.nexus Read Tree File in Nexus Format
dist.topo Topological Distances Between Two Trees
read.nexus.data Read Character Data In NEXUS Format
plot.correlogram Plot a Correlogram
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
ratogram Ratogram Computed by Nonparametric Rate Smoothing
ltt.plot Lineages Through Time Plot
multi2di Collapse and Resolve Multichotomies
root Roots Phylogenetic Trees
landplants Gene Tree of 36 Landplant rbcL Sequences
corBrownian Brownian Correlation Structure
nj Neighbor-Joining Tree Estimation
read.GenBank Read DNA Sequences from GenBank via Internet
rotate Rotate an Internal Branch of a Tree
theta.k Population Parameter THETA using Expected Number of Alleles
plot.correlogramList Plot several Correlograms
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
nuc.div Nucleotide Diversity
diversi.gof Tests of Constant Diversification Rates
seg.sites Find Segregating Sites in DNA Sequences
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
branching.times Branching Times of a Phylogenetic Tree
coalescent.intervals Coalescent Intervals
xenarthra Molecular Phylogeny of Living Xenarthrans
read.tree Read Tree File in Parenthetic Format
corClasses Phylogenetic Correlation Structures
reorder.phylo Internal Reordering of Trees
sh.test Shimodaira-Hasegawa Test
node.sons Get the list of Sons for a Node
consensus Concensus Trees
write.dna Write DNA Sequences in a File
write.nexus Write Tree File in Nexus Format
balance Balance of a Dichotomous Phylogenetic Tree
is.ultrametric Test if a Tree is Ultrametric
skylineplot Drawing Skyline Plot Graphs
chronogram Chronogram Computed by Nonparametric Rate Smoothing
gammaStat Gamma-Statistic of Pybus and Harvey
write.nexus.data Write Character Data In NEXUS Format
which.edge Identifies Edges of a Tree
howmanytrees Calculate Numbers of Phylogenetic Trees
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
opsin Gene Tree of 32 opsin Sequences
varcomp Compute Variance Component Estimates
mst Minimum Spanning Tree
yule.cov Fits the Yule Model With Covariates
plot.varcomp Plot Variance Components
rtree Generates Random Trees
mrca Find Most Recent Common Ancestors Between Pairs
summary.phylo Print Summary of a Phylogeny
skyline Skyline Plot Estimate of Effective Population Size
woodmouse Cytochrome b Gene Sequences of Woodmice
nodelabels Labelling the Nodes and the Tips of a Tree
write.tree Write Tree File in Parenthetic Format
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Date 2006-09-18
ZipData no
License GPL version 2 or newer
Packaged Mon Sep 18 15:43:34 2006; paradis

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