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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 as well as importing from BioConductor, and several tools such as Mantel's test, 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
as.alignment Conversion Among DNA Sequence Internal Formats
carnivora Carnivora body sizes and life history traits
makeLabel Label Management
c.phylo Building Lists of Trees
corPagel Pagel's ``lambda'' Correlation Structure
compar.gee Comparative Analysis with GEEs
DNAbin Manipulate DNA Sequences in Bit-Level Format
diversi.gof Tests of Constant Diversification Rates
as.phylo Conversion Among Tree and Network Objects
chronoMPL Molecular Dating With Mean Path Lengths
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
write.tree Write Tree File in Parenthetic Format
ape-package Analyses of Phylogenetics and Evolution
MPR Most Parsimonious Reconstruction
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
mat5M3ID Five Trees
mat5Mrand Five Independent Trees
corClasses Phylogenetic Correlation Structures
plot.varcomp Plot Variance Components
delta.plot Delta Plots
stree Generates Systematic Regular Trees
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
speciesTree Species Tree Estimation
cherry Number of Cherries and Null Models of Trees
SDM Construction of Consensus Distance Matrix With SDM
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
is.binary.tree Test for Binary Tree
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
subtrees All subtrees of a Phylogenetic Tree
CADM.global Congruence among distance matrices
branching.times Branching Times of a Phylogenetic Tree
mixedFontLabel Mixed Font Labels for Plotting
mst Minimum Spanning Tree
phymltest Fits a Bunch of Models with PhyML
opsin Gene Tree of 32 opsin Sequences
matexpo Matrix Exponential
def Definition of Vectors for Plotting or Annotating
edges Draw Additional Edges on a Plotted Tree
as.matching Conversion Between Phylo and Matching Objects
weight.taxo Define Similarity Matrix
mvr Minimum Variance Reduction
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
dist.dna Pairwise Distances from DNA Sequences
mantel.test Mantel Test for Similarity of Two Matrices
ace Ancestral Character Estimation
del.gaps Delete Alignment Gaps in DNA Sequences
nodepath Find Paths of Nodes
alex Alignment Explorer With Multiple Devices
mrca Find Most Recent Common Ancestors Between Pairs
kronoviz Plot Multiple Chronograms on the Same Scale
richness.yule.test Test of Diversification-Shift With the Yule Process
ape-internal Internal Ape Functions
plot.correlogram Plot a Correlogram
base.freq Base frequencies from DNA Sequences
rtree Generates Random Trees
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
corBrownian Brownian Correlation Structure
landplants Gene Tree of 36 Landplant rbcL Sequences
rTraitCont Continuous Character Simulation
Initialize.corPhyl Initialize a `corPhyl' Structure Object
data.nex NEXUS Data Example
zoom Zoom on a Portion of a Phylogeny
howmanytrees Calculate Numbers of Phylogenetic Trees
reorder.phylo Internal Reordering of Trees
diversity.contrast.test Diversity Contrast Test
varcomp Compute Variance Component Estimates
rTraitDisc Discrete Character Simulation
lmorigin Multiple regression through the origin
write.dna Write DNA Sequences in a File
root Roots Phylogenetic Trees
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
skylineplot Drawing Skyline Plot Graphs
is.ultrametric Test if a Tree is Ultrametric
trex Tree Explorer With Multiple Devices
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
woodmouse Cytochrome b Gene Sequences of Woodmice
write.nexus Write Tree File in Nexus Format
node.depth Depth and Heights of Nodes and Tips
nj Neighbor-Joining Tree Estimation
rotate Swapping Sister Clades
plot.phylo Plot Phylogenies
rTraitMult Multivariate Character Simulation
vcv Phylogenetic Variance-covariance or Correlation Matrix
consensus Concensus Trees
gammaStat Gamma-Statistic of Pybus and Harvey
compar.cheverud Cheverud's Comparative Method
compar.lynch Lynch's Comparative Method
identify.phylo Graphical Identification of Nodes and Tips
dbd Probability Density Under Birth--Death Models
ltt.plot Lineages Through Time Plot
mat3 Three Matrices
pic.ortho Phylogenetically Independent Orthonormal Contrasts
axisPhylo Axis on Side of Phylogeny
read.nexus.data Read Character Data In NEXUS Format
seg.sites Find Segregating Sites in DNA Sequences
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
varCompPhylip Variance Components with Orthonormal Contrasts
write.nexus.data Write Character Data in NEXUS Format
print.phylo Compact Display of a Phylogeny
reconstruct Continuous Ancestral Character Estimation
yule Fits the Yule Model to a Phylogenetic Tree
Moran.I Moran's I Autocorrelation Index
triangMtd Tree Reconstruction Based on the Triangles Method
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
bd.time Time-Dependent Birth-Death Models
corGrafen Grafen's (1989) Correlation Structure
yule.cov Fits the Yule Model With Covariates
ladderize Ladderize a Tree
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
diversi.time Analysis of Diversification with Survival Models
as.bitsplits Split Frequencies and Conversion Among Split Classes
phydataplot Tree Annotation
dist.topo Topological Distances Between Two Trees
read.GenBank Read DNA Sequences from GenBank via Internet
compute.brtime Compute and Set Branching Times
correlogram.formula Phylogenetic Correlogram
multiphylo Manipulating Lists of Trees
balance Balance of a Dichotomous Phylogenetic Tree
FastME Tree Estimation Based on the Minimum Evolution Algorithm
is.monophyletic Is Group Monophyletic
LTT Theoretical Lineage-Through Time Plots
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
treePop Tree Popping
pcoa Principal Coordinate Analysis
image.DNAbin Plot of DNA Sequence Alignement
read.dna Read DNA Sequences in a File
bind.tree Binds Trees
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
unique.multiPhylo Revomes Duplicate Trees
read.caic Read Tree File in CAIC Format
read.tree Read Tree File in Parenthetic Format
read.nexus Read Tree File in Nexus Format
clustal Multiple Sequence Alignment with External Applications
where Find Patterns in DNA Sequences
yule.time Fits the Time-Dependent Yule Model
collapsed.intervals Collapsed Coalescent Intervals
rtt Root a Tree by Root-to-Tip Regression
skyline Skyline Plot Estimate of Effective Population Size
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
which.edge Identifies Edges of a Tree
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
pic Phylogenetically Independent Contrasts
vcv2phylo Variance-Covariance Matrix to Tree
summary.phylo Print Summary of a Phylogeny
additive Incomplete Distance Matrix Filling
all.equal.phylo Global Comparison of two Phylogenies
add.scale.bar Add a Scale Bar to a Phylogeny Plot
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
chronopl Molecular Dating With Penalized Likelihood
coalescent.intervals Coalescent Intervals
compute.brlen Branch Lengths Computation
dist.gene Pairwise Distances from Genetic Data
ewLasso Incomplete distances and edge weights of unrooted topology
multi2di Collapse and Resolve Multichotomies
collapse.singles Collapse Single Nodes
corBlomberg Blomberg et al.'s Correlation Structure
makeNodeLabel Makes Node Labels
chiroptera Bat Phylogeny
corMartins Martins's (1997) Correlation Structure
evonet Evolutionary Networks
is.compatible Check Compatibility of Splits
parafit Test of host-parasite coevolution
drop.tip Remove Tips in a Phylogenetic Tree
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
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