ape v2.3-1

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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. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

Functions in ape

Name Description
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
mat3 Three Matrices
as.phylo Conversion Among Tree Objects
read.nexus.data Read Character Data In NEXUS Format
which.edge Identifies Edges of a Tree
sh.test Shimodaira-Hasegawa Test
add.scale.bar Add a Scale Bar to a Phylogeny Plot
del.gaps Delete Alignment Gaps in DNA Sequences
dist.dna Pairwise Distances from DNA Sequences
rotate Swapping sister clades
yule Fits Yule Model to a Phylogenetic Tree
base.freq Base frequencies from DNA Sequences
ladderize Ladderize a Tree
skyline Skyline Plot Estimate of Effective Population Size
DNAbin Manipulate DNA Sequences in Bit-Level Format
cherry Number of Cherries and Null Models of Trees
all.equal.phylo Global Comparison of two Phylogenies
branching.times Branching Times of a Phylogenetic Tree
dist.gene Pairwise Distances from Genetic Data
coalescent.intervals Coalescent Intervals
collapsed.intervals Collapsed Coalescent Intervals
corBlomberg Blomberg et al.'s Correlation Structure
is.ultrametric Test if a Tree is Ultrametric
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
chiroptera Bat Phylogeny
print.phylo Compact Display of a Phylogeny
mrca Find Most Recent Common Ancestors Between Pairs
plot.correlogram Plot a Correlogram
yule.cov Fits the Yule Model With Covariates
varcomp Compute Variance Component Estimates
heterozygosity Heterozygosity at a Locus Using Gene Frequencies
ltt.plot Lineages Through Time Plot
bind.tree Binds Trees
plot.varcomp Plot Variance Components
gammaStat Gamma-Statistic of Pybus and Harvey
mat5Mrand Five Independent Trees
howmanytrees Calculate Numbers of Phylogenetic Trees
read.dna Read DNA Sequences in a File
yule.time Fits the Time-Dependent Yule Model
write.dna Write DNA Sequences in a File
theta.h Population Parameter THETA using Homozygosity
write.tree Write Tree File in Parenthetic Format
CADM.global Congruence among distance matrices
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
read.nexus Read Tree File in Nexus Format
plot.phylo Plot Phylogenies
corClasses Phylogenetic Correlation Structures
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
write.nexus Write Tree File in Nexus Format
dist.topo Topological Distances Between Two Trees
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
FastME Tree Estimation Based on the Minimum Evolution Algorithm
rtree Generates Random Trees
compar.cheverud Cheverud's Comparative Method
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
NPRS.criterion Objective Function Employed in Nonparametric Rate Smoothing
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
phymltest Fits a Bunch of Models with PhyML
correlogram.formula Phylogenetic Correlogram
is.binary.tree Test for Binary Tree
woodmouse Cytochrome b Gene Sequences of Woodmice
summary.phylo Print Summary of a Phylogeny
mlphylo Estimating Phylogenies by Maximum Likelihood
collapse.singles Collapse Single Nodes
nuc.div Nucleotide Diversity
plot.ancestral Plot Ancestral Character Values on a Tree
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
as.matching Conversion Between Phylo and Matching Objects
axisPhylo Axis on Side of Phylogeny
compar.lynch Lynch's Comparative Method
GC.content Content in GC from DNA Sequences
identify.phylo Graphical Identification of Nodes and Tips
theta.s Population Parameter THETA using Segregating Sites in DNA Sequences
carnivora Carnivora body sizes and life history traits
drop.tip Remove Tips in a Phylogenetic Tree
matexpo Matrix Exponential
skylineplot Drawing Skyline Plot Graphs
Initialize.corPhyl Initialize a `corPhyl' Structure Object
chronopl Molecular Dating With Penalized Likelihood
subtrees All subtrees of a Phylogenetic Tree
compar.gee Comparative Analysis with GEEs
as.alignment Conversion Among DNA Sequence Internal Formats
landplants Gene Tree of 36 Landplant rbcL Sequences
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
compute.brlen Branch Lengths Computation
is.monophyletic Is Group Monophyletic
unique.multiPhylo Revomes Duplicate Trees
theta.k Population Parameter THETA using Expected Number of Alleles
seg.sites Find Segregating Sites in DNA Sequences
read.caic Read Tree File in CAIC Format
read.tree Read Tree File in Parenthetic Format
write.nexus.data Write Character Data In NEXUS Format
ape-package Analyses of Phylogenetics and Evolution
consensus Concensus Trees
nj Neighbor-Joining Tree Estimation
balance Balance of a Dichotomous Phylogenetic Tree
ace Ancestral Character Estimation
node.depth Depth of Nodes and Tips
mst Minimum Spanning Tree
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
evolve.phylo Ancestral Character Simulation
ape-internal Internal Ape Functions
corBrownian Brownian Correlation Structure
chronogram Chronogram Computed by Nonparametric Rate Smoothing
data.nex NEXUS Data Example
multi2di Collapse and Resolve Multichotomies
makeLabel Label Management
corGrafen Grafen's (1989) Correlation Structure
mat5M3ID Five Trees
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
reorder.phylo Internal Reordering of Trees
opsin Gene Tree of 32 opsin Sequences
corMartins Martins's (1997) Correlation Structure
ratogram Ratogram Computed by Nonparametric Rate Smoothing
diversi.gof Tests of Constant Diversification Rates
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
root Roots Phylogenetic Trees
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
read.GenBank Read DNA Sequences from GenBank via Internet
weight.taxo Define Similarity Matrix
Moran.I Moran's I Autocorrelation Index
DNAmodel Defines Models of DNA Evolution
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
corPagel Pagel's ``lambda'' Correlation Structure
mantel.test Mantel Test for Similarity of Two Matrices
diversi.time Analysis of Diversification with Survival Models
chronoMPL Molecular Dating With Mean Path Lengths
makeNodeLabel Makes Node Labels
pic Phylogenetically Independent Contrasts
vcv.phylo Phylogenetic Variance-covariance or Correlation Matrix
zoom Zoom on a Portion of a Phylogeny
klastorin Klastorin's (1982) method for classifying genes as suggested by Misawa and Tajima (2000)
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