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