ape v2.2-3

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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, and ME methods.

Functions in ape

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