ape v3.1-1

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