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