ape v2.0-1


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