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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 allelic and nucleotide data, 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. 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
add.scale.bar Add a Scale Bar to a Phylogeny Plot
ape-package Analyses of Phylogenetics and Evolution
as.phylo.formula Conversion from Taxonomy Variables to Phylogenetic Trees
balance Balance of a Dichotomous Phylogenetic Tree
bind.tree Binds Trees
axisPhylo Axis on Side of Phylogeny
base.freq Base frequencies from DNA Sequences
bd.time Time-Dependent Birth-Death Models
as.bitsplits Split Frequencies and Conversion Among Split Classes
bd.ext Extended Version of the Birth-Death Models to Estimate Speciation and Extinction Rates
as.phylo Conversion Among Tree and Network Objects
as.matching Conversion Between Phylo and Matching Objects
birthdeath Estimation of Speciation and Extinction Rates With Birth-Death Models
BIONJ Tree Estimation Based on an Improved Version of the NJ Algorithm
carnivora Carnivora body sizes and life history traits
c.phylo Building Lists of Trees
CADM.global Congruence among distance matrices
collapse.singles Collapse Single Nodes
collapsed.intervals Collapsed Coalescent Intervals
checkValidPhylo Check the Structure of a "phylo" Object
clustal Multiple Sequence Alignment with External Applications
ape-internal Internal Ape Functions
coalescent.intervals Coalescent Intervals
chronos Molecular Dating by Penalised Likelihood and Maximum Likelihood
chronoMPL Molecular Dating With Mean Path Lengths
chiroptera Bat Phylogeny
cherry Number of Cherries and Null Models of Trees
alex Alignment Explorer With Multiple Devices
chronopl Molecular Dating With Penalized Likelihood
boot.phylo Tree Bipartition and Bootstrapping Phylogenies
ace Ancestral Character Estimation
AAbin Amino Acid Sequences
all.equal.phylo Global Comparison of two Phylogenies
alview Print DNA or AA Sequence Alignement
additive Incomplete Distance Matrix Filling
cophyloplot Plots two phylogenetic trees face to face with links between the tips.
compar.ou Ornstein--Uhlenbeck Model for Continuous Characters
compute.brtime Compute and Set Branching Times
compute.brlen Branch Lengths Computation
compar.gee Comparative Analysis with GEEs
compar.lynch Lynch's Comparative Method
compar.cheverud Cheverud's Comparative Method
bird.orders Phylogeny of the Orders of Birds From Sibley and Ahlquist
branching.times Branching Times of a Phylogenetic Tree
consensus Concensus Trees
corBlomberg Blomberg et al.'s Correlation Structure
checkAlignment Check DNA Alignments
cophenetic.phylo Pairwise Distances from a Phylogenetic Tree
as.alignment Conversion Among DNA Sequence Internal Formats
bird.families Phylogeny of the Families of Birds From Sibley and Ahlquist
data.nex NEXUS Data Example
corBrownian Brownian Correlation Structure
corGrafen Grafen's (1989) Correlation Structure
corMartins Martins's (1997) Correlation Structure
def Definition of Vectors for Plotting or Annotating
dbd Probability Density Under Birth--Death Models
corClasses Phylogenetic Correlation Structures
dist.gene Pairwise Distances from Genetic Data
corPagel Pagel's ``lambda'' Correlation Structure
dist.topo Topological Distances Between Two Trees
DNAbin Manipulate DNA Sequences in Bit-Level Format
drop.tip Remove Tips in a Phylogenetic Tree
diversi.gof Tests of Constant Diversification Rates
DNAbin2indel Recode Blocks of Indels
dist.dna Pairwise Distances from DNA Sequences
edges Draw Additional Edges on a Plotted Tree
gammaStat Gamma-Statistic of Pybus and Harvey
Initialize.corPhyl Initialize a `corPhyl' Structure Object
del.gaps Delete Alignment Gaps in DNA Sequences
correlogram.formula Phylogenetic Correlogram
diversity.contrast.test Diversity Contrast Test
diversi.time Analysis of Diversification with Survival Models
FastME Tree Estimation Based on the Minimum Evolution Algorithm
ewLasso Incomplete distances and edge weights of unrooted topology
identify.phylo Graphical Identification of Nodes and Tips
image.DNAbin Plot of DNA Sequence Alignement
is.binary.tree Test for Binary Tree
is.monophyletic Is Group Monophyletic
label2table Label Management
landplants Gene Tree of 36 Landplant rbcL Sequences
is.ultrametric Test if a Tree is Ultrametric
mat5Mrand Five Independent Trees
hivtree Phylogenetic Tree of 193 HIV-1 Sequences
delta.plot Delta Plots
evonet Evolutionary Networks
howmanytrees Calculate Numbers of Phylogenetic Trees
ltt.plot Lineages Through Time Plot
ladderize Ladderize a Tree
matexpo Matrix Exponential
mcmc.popsize Reversible Jump MCMC to Infer Demographic History
mat5M3ID Five Trees
mat3 Three Matrices
makeLabel Label Management
mst Minimum Spanning Tree
mrca Find Most Recent Common Ancestors Between Pairs
mvr Minimum Variance Reduction
kronoviz Plot Multiple Chronograms on the Same Scale
mixedFontLabel Mixed Font Labels for Plotting
Moran.I Moran's I Autocorrelation Index
MPR Most Parsimonious Reconstruction
nj Neighbor-Joining Tree Estimation
multiphylo Manipulating Lists of Trees
njs Tree Reconstruction from Incomplete Distances With NJ* or bio-NJ*
is.compatible Check Compatibility of Splits
lmorigin Multiple regression through the origin
makeNodeLabel Makes Node Labels
LTT Theoretical Lineage-Through Time Plots
mcconwaysims.test McConway-Sims Test of Homogeneous Diversification
mantel.test Mantel Test for Similarity of Two Matrices
parafit Test of host-parasite coevolution
nodepath Find Paths of Nodes
pic Phylogenetically Independent Contrasts
pcoa Principal Coordinate Analysis
nodelabels Labelling the Nodes, Tips, and Edges of a Tree
multi2di Collapse and Resolve Multichotomies
opsin Gene Tree of 32 opsin Sequences
phydataplot Tree Annotation
pic.ortho Phylogenetically Independent Orthonormal Contrasts
node.depth Depth and Heights of Nodes and Tips
phymltest Fits a Bunch of Models with PhyML
print.phylo Compact Display of a Phylogeny
read.caic Read Tree File in CAIC Format
plot.correlogram Plot a Correlogram
plot.phylo.extra Extra Fuctions to Plot and Annotate Phylogenies
read.GenBank Read DNA Sequences from GenBank via Internet
reconstruct Continuous Ancestral Character Estimation
rTraitCont Continuous Character Simulation
plot.phylo Plot Phylogenies
read.dna Read DNA Sequences in a File
root Roots Phylogenetic Trees
rotate Swapping Sister Clades
reorder.phylo Internal Reordering of Trees
rlineage Tree Simulation Under the Time-Dependent Birth--Death Models
rTraitMult Multivariate Character Simulation
rTraitDisc Discrete Character Simulation
read.tree Read Tree File in Parenthetic Format
read.nexus.data Read Character Data In NEXUS Format
richness.yule.test Test of Diversification-Shift With the Yule Process
slowinskiguyer.test Slowinski-Guyer Test of Homogeneous Diversification
speciesTree Species Tree Estimation
read.nexus Read Tree File in Nexus Format
vcv2phylo Variance-Covariance Matrix to Tree
weight.taxo Define Similarity Matrix
plot.varcomp Plot Variance Components
subtreeplot Zoom on a Portion of a Phylogeny by Successive Clicks
stree Generates Systematic Regular Trees
unique.multiPhylo Revomes Duplicate Trees
varcomp Compute Variance Component Estimates
trans Translation from DNA to Amino Acid Sequences
woodmouse Cytochrome b Gene Sequences of Woodmice
treePop Tree Popping
write.nexus Write Tree File in Nexus Format
write.nexus.data Write Character Data in NEXUS Format
write.dna Write DNA Sequences in a File
rtree Generates Random Trees
skyline Skyline Plot Estimate of Effective Population Size
yule Fits the Yule Model to a Phylogenetic Tree
rtt Root a Tree by Root-to-Tip Regression
skylineplot Drawing Skyline Plot Graphs
subtrees All subtrees of a Phylogenetic Tree
summary.phylo Print Summary of a Phylogeny
triangMtd Tree Reconstruction Based on the Triangles Method
trex Tree Explorer With Multiple Devices
zoom Zoom on a Portion of a Phylogeny
where Find Patterns in DNA Sequences
seg.sites Find Segregating Sites in DNA Sequences
SDM Construction of Consensus Distance Matrix With SDM
which.edge Identifies Edges of a Tree
vcv Phylogenetic Variance-covariance or Correlation Matrix
varCompPhylip Variance Components with Orthonormal Contrasts
yule.time Fits the Time-Dependent Yule Model
write.tree Write Tree File in Parenthetic Format
yule.cov Fits the Yule Model With Covariates
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