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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 DNA sequences, 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, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. 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, MAFFT) whose results are returned into R.

Functions in ape

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