ape v2.1-3

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