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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
as.alignment Conversion Among DNA Sequence Internal Formats
additive Incomplete Distance Matrix Filling
balance Balance of a Dichotomous Phylogenetic Tree
as.phylo Conversion Among Tree and Network Objects
chronoMPL Molecular Dating With Mean Path Lengths
binaryPGLMM Phylogenetic Generalized Linear Mixed Model for Binary Data
alview Print DNA Sequence Alignements
is.ultrametric Test if a Tree is Ultrametric
checkValidPhylo Check the Structure of a "phylo" Object
DNAbin2indel Recode Blocks of Indels
chiroptera Bat Phylogeny
chronopl Molecular Dating With Penalized Likelihood
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
compar.gee Comparative Analysis with GEEs
Moran.I Moran's I Autocorrelation Index
edges Draw Additional Edges on a Plotted Tree
dbd Probability Density Under Birth--Death Models
makeNodeLabel Makes Node Labels
corphylo Correlations among Multiple Traits with Phylogenetic Signal
carnivora Carnivora body sizes and life history traits
as.matching Conversion Between Phylo and Matching Objects
bind.tree Binds Trees
compar.lynch Lynch's Comparative Method
alex Alignment Explorer With Multiple Devices
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
coalescent.intervals Coalescent Intervals
axisPhylo Axis on Side of Phylogeny
reorder.phylo Internal Reordering of Trees
del.gaps Delete Alignment Gaps in DNA Sequences
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
bd.time Time-Dependent Birth-Death Models
corMartins Martins's (1997) Correlation Structure
compute.brlen Branch Lengths Computation
collapse.singles Collapse Single Nodes
kronoviz Plot Multiple Chronograms on the Same Scale
dist.dna Pairwise Distances from DNA Sequences
diversi.time Analysis of Diversification with Survival Models
ladderize Ladderize a Tree
clustal Multiple Sequence Alignment with External Applications
consensus Concensus Trees
all.equal.phylo Global Comparison of two Phylogenies
ace Ancestral Character Estimation
node.depth Depth and Heights of Nodes and Tips
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
as.bitsplits Split Frequencies and Conversion Among Split Classes
read.caic Read Tree File in CAIC Format
varCompPhylip Variance Components with Orthonormal Contrasts
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
multi2di Collapse and Resolve Multichotomies
ewLasso Incomplete distances and edge weights of unrooted topology
SDM Construction of Consensus Distance Matrix With SDM
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
collapsed.intervals Collapsed Coalescent Intervals
corBrownian Brownian Correlation Structure
identify.phylo Graphical Identification of Nodes and Tips
data.nex NEXUS Data Example
trex Tree Explorer With Multiple Devices
read.nexus Read Tree File in Nexus Format
gammaStat Gamma-Statistic of Pybus and Harvey
corGrafen Grafen's (1989) Correlation Structure
drop.tip Remove Tips in a Phylogenetic Tree
rTraitCont Continuous Character Simulation
read.GenBank Read DNA Sequences from GenBank via Internet
opsin Gene Tree of 32 opsin Sequences
corBlomberg Blomberg et al.'s Correlation Structure
seg.sites Find Segregating Sites in DNA Sequences
label2table Label Management
howmanytrees Calculate Numbers of Phylogenetic Trees
is.binary.tree Test for Binary Tree
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
branching.times Branching Times of a Phylogenetic Tree
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
Initialize.corPhyl Initialize a `corPhyl' Structure Object
plot.correlogram Plot a Correlogram
matexpo Matrix Exponential
c.phylo Building Lists of Trees
CADM.global Congruence among distance matrices
dist.gene Pairwise Distances from Genetic Data
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
ape-internal Internal Ape Functions
mat3 Three Matrices
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
skyline Skyline Plot Estimate of Effective Population Size
rtree Generates Random Trees
richness.yule.test Test of Diversification-Shift With the Yule Process
print.phylo Compact Display of a Phylogeny
write.dna Write DNA Sequences in a File
mrca Find Most Recent Common Ancestors Between Pairs
corClasses Phylogenetic Correlation Structures
mst Minimum Spanning Tree
which.edge Identifies Edges of a Tree
zoom Zoom on a Portion of a Phylogeny
skylineplot Drawing Skyline Plot Graphs
ltt.plot Lineages Through Time Plot
subtrees All subtrees of a Phylogenetic Tree
unique.multiPhylo Revomes Duplicate Trees
triangMtd Tree Reconstruction Based on the Triangles Method
speciesTree Species Tree Estimation
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
diversi.gof Tests of Constant Diversification Rates
summary.phylo Print Summary of a Phylogeny
mvr Minimum Variance Reduction
multiphylo Manipulating Lists of Trees
vcv2phylo Variance-Covariance Matrix to Tree
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
is.monophyletic Is Group Monophyletic
yule.time Fits the Time-Dependent Yule Model
read.dna Read DNA Sequences in a File
where Find Patterns in DNA Sequences
write.tree Write Tree File in Parenthetic Format
nodepath Find Paths of Nodes
write.nexus.data Write Character Data in NEXUS Format
delta.plot Delta Plots
cherry Number of Cherries and Null Models of Trees
is.compatible Check Compatibility of Splits
pic Phylogenetically Independent Contrasts
treePop Tree Popping
base.freq Base frequencies from DNA Sequences
rTraitMult Multivariate Character Simulation
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
phymltest Fits a Bunch of Models with PhyML
corPagel Pagel's ``lambda'' Correlation Structure
write.nexus Write Tree File in Nexus Format
ape-package Analyses of Phylogenetics and Evolution
mat5Mrand Five Independent Trees
MPR Most Parsimonious Reconstruction
plot.phylo Plot Phylogenies
read.tree Read Tree File in Parenthetic Format
diversity.contrast.test Diversity Contrast Test
evonet Evolutionary Networks
mantel.test Mantel Test for Similarity of Two Matrices
makeLabel Label Management
image.DNAbin Plot of DNA Sequence Alignement
plot.varcomp Plot Variance Components
lmorigin Multiple regression through the origin
rTraitDisc Discrete Character Simulation
read.nexus.data Read Character Data In NEXUS Format
reconstruct Continuous Ancestral Character Estimation
stree Generates Systematic Regular Trees
yule.cov Fits the Yule Model With Covariates
rtt Root a Tree by Root-to-Tip Regression
woodmouse Cytochrome b Gene Sequences of Woodmice
nj Neighbor-Joining Tree Estimation
compute.brtime Compute and Set Branching Times
vcv Phylogenetic Variance-covariance or Correlation Matrix
phydataplot Tree Annotation
varcomp Compute Variance Component Estimates
rotate Swapping Sister Clades
DNAbin Manipulate DNA Sequences in Bit-Level Format
add.scale.bar Add a Scale Bar to a Phylogeny Plot
def Definition of Vectors for Plotting or Annotating
FastME Tree Estimation Based on the Minimum Evolution Algorithm
mat5M3ID Five Trees
mixedFontLabel Mixed Font Labels for Plotting
compar.cheverud Cheverud's Comparative Method
pcoa Principal Coordinate Analysis
pic.ortho Phylogenetically Independent Orthonormal Contrasts
parafit Test of host-parasite coevolution
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
correlogram.formula Phylogenetic Correlogram
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
weight.taxo Define Similarity Matrix
yule Fits the Yule Model to a Phylogenetic Tree
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
LTT Theoretical Lineage-Through Time Plots
dist.topo Topological Distances Between Two Trees
root Roots Phylogenetic Trees
landplants Gene Tree of 36 Landplant rbcL Sequences
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