ape v5.1

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by Emmanuel Paradis View Source

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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Vignettes of ape

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MoranI.Rnw
ape.bib
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Details

Date	2018-04-03
LinkingTo	Rcpp
ZipData	no
License	GPL (>= 2)
URL	http://ape-package.ird.fr/
NeedsCompilation	yes
Packaged	2018-04-03 13:27:51 UTC; paradis
Repository	CRAN
Date/Publication	2018-04-04 22:16:00 UTC

suggests	expm , gee , igraph
imports	graphics , lattice , methods , nlme , parallel , Rcpp (>= 0.12.0) , stats , tools , utils
depends	R (>= 3.2.0)
Contributors	Anthony Ives, Joseph Brown, Ben Bolker, Julien Claude, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian Strimmer, Hoa Sien Cuong, Damien de Vienne, Rosemary McCloskey, Simon Blomberg, Gilles Didier, Manuela Royer-Carenzi, Bradley Jones, RJ Ewing, Franz Krah, Thomas Guillerme