ape v2.6-1

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