ape v2.2-2


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