ape v3.3


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Analyses of Phylogenetics and Evolution

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