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