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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) whose results are returned into R.

Functions in ape

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