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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, 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
compar.lynch Lynch's Comparative Method
base.freq Base frequencies from DNA Sequences
plot.phylo Plot Phylogenies
ltt.plot Lineages Through Time Plot
opsin Gene Tree of 32 opsin Sequences
skylineplot Drawing Skyline Plot Graphs
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
drop.tip Remove Tips in a Phylogenetic Tree
write.dna Write DNA Sequences in a File
chronogram Chronogram Computed by Nonparametric Rate Smoothing
branching.times Branching Times of a Phylogenetic Tree
dist.gene Pairwise Distances from Genetic Data
dist.phylo Pairwise Distances from a Phylogenetic Tree
is.binary.tree Test for Binary Tree
dist.dna Pairwise Distances from DNA Sequences
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
cherry Number of Cherries and Null Models of Trees
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
read.GenBank Read DNA Sequences from GenBank via Internet
write.tree Write Tree File in Parenthetic Format
ratogram Ratogram Computed by Nonparametric Rate Smoothing
compar.gee Comparative Analysis with GEEs
Correlogram Compute a correlogram
as.phylo Conversion between "phylo" and "hclust" trees
summary.phylo Print Summary of a Phylogeny
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
mst Minimum Spanning Tree
read.dna Read DNA Sequences in a File
add.scale.bar Add a Scale Bar to a Phylogeny Plot
read.tree Read Tree File in Parenthetic Format
all.equal.phylo Global Comparison of two Phylogenies
diversi.time Analysis of Diversification with Survival Models
Initialize.corPhyl Initialize a 'corPhyl' Structure Object
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
carnivora Carnivora body sizes and life history traits
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
ape-internal Internal Ape Functions
theta.h Population Parameter THETA using Homozygosity
mantel.test Mantel Test for Similarity of Two Matrices
landplants Gene Tree of 36 Landplant rbcL Sequences
corBrownian Brownian Correlation Structure
diversi.gof Tests of Constant Diversification Rates
gamma.stat Gamma-Statistic of Pybus and Harvey
collapse.singles Collapse Single Nodes
bind.tree Binds Trees
howmanytrees Calculate Numbers of Phylogenetic Trees
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
is.ultrametric Test if a Tree is Ultrametric
pic Phylogenetically Independent Contrasts
panel.superpose.correlogram Lattice panel used in 'plot.correlogramList'.
balance Balance of a Dichotomous Phylogenetic Tree
sh.test Shimodaira-Hasegawa Test
plot.ancestral Plot Ancestral Character Values on a Tree
read.nexus Read Tree File in Nexus Format
collapsed.intervals Collapsed Coalescent Intervals
compute.brlen Branch Lengths Computation
plot.varcomp Plot Variance Components
mrca Find Most Recent Common Ancestors Between Pairs
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
as.matching Conversion Between Phylo and Matching Objects
GC.content Content in GC from DNA Sequences
which.edge Identifies Edges of a Tree
corGrafen Grafen's (1989) Correlation Structure
ace Ancestral Character Estimation
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
write.nexus Write Tree File in Nexus Format
coalescent.intervals Coalescent Intervals
node.depth Depth of Nodes and Tips
as.alignment Conversion Among DNA Sequence Internal Formats
xenarthra Molecular Phylogeny of Living Xenarthrans
root Roots Phylogenetic Trees
DNAbin Manipulate DNA Sequences in Bit-Level Format
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
woodmouse Cytochrome b Gene Sequences of Woodmice
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
Moran.I Moran's I Autocorrelation Index
theta.k Population Parameter THETA using Expected Number of Alleles
evolve.phylo Ancestral Character Simulation
ladderize Ladderize a Tree
corMartins Martins's (1997) Correlation Structure
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
corClasses Phylogenetic Correlation Structures
chronopl Molecular Dating With Penalized Likelihood
varcomp Compute Variance Component Estimates
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
nj Neighbor-Joining Tree Estimation
DNAmodel Defines Models of DNA Evolution
mlphylo Estimating Phylogenies by Maximum Likelihood
read.nexus.data Read Character Data In NEXUS Format
weight.taxo Pairwise Distances from a Taxonomic Level
consensus Concensus Trees
reorder.phylo Internal Reordering of Trees
yule Fits Yule Model to a Phylogenetic Tree
skyline Skyline Plot Estimate of Effective Population Size
multi2di Collapse and Resolve Multichotomies
dist.topo Topological Distances Between Two Trees
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
chiroptera Bat Phylogeny
seg.sites Find Segregating Sites in DNA Sequences
yule.cov Fits the Yule Model With Covariates
phymltest Fits a Bunch of Models with PHYML
nuc.div Nucleotide Diversity
data.nex NEXUS Data Example
print.phylo Compact Display of a Phylogeny
zoom Zoom on a Portion of a Phylogeny
discrete.dist Taxonomic Level from a Pairwise Distances Matrix
axisPhylo Axis on Side of Phylogeny
read.caic Read Tree File in CAIC Format
plot.correlogramList Plot several Correlograms
gammaStat Gamma-Statistic of Pybus and Harvey
write.nexus.data Write Character Data In NEXUS Format
plot.correlogram Plot a Correlogram
compar.cheverud Cheverud's Comparative Method
rtree Generates Random Trees
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Date 2003-06-06
License GPL version 2 or newer
depends gee
Contributors Emmanuel Paradis

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