ape v3.0-3

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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, ancestral character analyses, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading and writing nucleotide sequences, and several tools such as Mantel's test, minimum spanning tree, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Functions in ape

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