ape v5.3

Monthly downloads

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
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
No Results!

Vignettes of ape

Name
MoranI.Rnw
ape.bib
No Results!

Last month downloads

Details

Date	2019-03-13
LinkingTo	Rcpp
ZipData	no
License	GPL (>= 2)
URL	http://ape-package.ird.fr/
NeedsCompilation	yes
Packaged	2019-03-13 22:28:57 UTC; paradis
Repository	CRAN
Date/Publication	2019-03-17 07:14:59 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, Eric Marcon, Gilles Didier, Manuela Royer-Carenzi, Bradley Jones, RJ Ewing, Franz Krah, Thomas Guillerme