ape v5.0

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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
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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Vignettes of ape

Name
MoranI.Rnw
ape.bib
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Details

Date	2017-10-04
LinkingTo	Rcpp
ZipData	no
License	GPL (>= 2)
URL	http://ape-package.ird.fr/
NeedsCompilation	yes
Packaged	2017-10-04 16:39:18 UTC; paradis
Repository	CRAN
Date/Publication	2017-10-30 15:36:18 UTC

suggests	expm , gee
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