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