ape v2.0-2

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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 mean path lengths, non-parametric rate smoothing and penalized likelihood, classifying genes in trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done with the NJ, BIONJ, ME, and ML methods.

Functions in ape

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