ape: 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, MAFFT) whose results are returned into R.

Author
Emmanuel Paradis [aut, cre, cph], Simon Blomberg [aut, cph], Ben Bolker [aut, cph], Julien Claude [aut, cph], Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph], Benoit Durand [aut, cph], Julien Dutheil [aut, cph], Olivier Gascuel [aut, cph], Christoph Heibl [aut, cph], Anthony Ives [aut, cph], Bradley Jones [aut, cph], Daniel Lawson [aut, cph], Vincent Lefort [aut, cph], Pierre Legendre [aut, cph], Jim Lemon [aut, cph], Rosemary McCloskey [aut, cph], Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph], Korbinian Strimmer [aut, cph], Damien de Vienne [aut, cph]
Date of publication
2016-12-01 17:40:32
Maintainer
Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
License
GPL (>= 2)
Version
4.0
URLs

View on CRAN

Man pages

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

Files in this package

ape
ape/COPYING
ape/inst
ape/inst/CITATION
ape/inst/doc
ape/inst/doc/MoranI.pdf
ape/inst/doc/MoranI.R
ape/inst/doc/MoranI.Rnw
ape/src
ape/src/Makevars
ape/src/NNI.c
ape/src/TBR.c
ape/src/pic.c
ape/src/nj.c
ape/src/bipartition.c
ape/src/heap.c
ape/src/delta_plot.c
ape/src/tree_build.c
ape/src/ewLasso.c
ape/src/mvrs.c
ape/src/bNNI.c
ape/src/mvr.c
ape/src/read_dna.c
ape/src/me_ols.c
ape/src/mat_expo.c
ape/src/SPR.c
ape/src/njs.c
ape/src/additive.c
ape/src/rTrait.c
ape/src/bionjs.c
ape/src/plot_phylo.c
ape/src/treePop.c
ape/src/bitsplits.c
ape/src/dist_nodes.c
ape/src/tree_phylo.c
ape/src/me_balanced.c
ape/src/reorder_phylo.c
ape/src/me.h
ape/src/dist_dna.c
ape/src/BIONJ.c
ape/src/triangMtds.c
ape/src/triangMtd.c
ape/src/ape.h
ape/src/ultrametric.c
ape/src/me.c
ape/src/ape.c
ape/NAMESPACE
ape/NEWS
ape/data
ape/data/cynipids.rda
ape/data/lmorigin.ex1.rda
ape/data/bird.families.rda
ape/data/carnivora.csv.gz
ape/data/mat5M3ID.RData
ape/data/chiroptera.rda
ape/data/hivtree.table.txt.gz
ape/data/bird.orders.rda
ape/data/hivtree.newick.rda
ape/data/lice.D.rda
ape/data/lmorigin.ex2.rda
ape/data/mat3.RData
ape/data/gopher.D.rda
ape/data/woodmouse.rda
ape/data/HP.links.rda
ape/data/mat5Mrand.RData
ape/R
ape/R/plot.phylo.R
ape/R/biplot.pcoa.R
ape/R/balance.R
ape/R/read.dna.R
ape/R/read.nexus.data.R
ape/R/zoom.R
ape/R/phymltest.R
ape/R/is.binary.tree.R
ape/R/is.monophyletic.R
ape/R/ace.R
ape/R/rtree.R
ape/R/compute.brtime.R
ape/R/dbd.R
ape/R/me.R
ape/R/Cheverud.R
ape/R/skylineplot.R
ape/R/def.R
ape/R/compar.lynch.R
ape/R/CDF.birth.death.R
ape/R/gammaStat.R
ape/R/chronopl.R
ape/R/cophyloplot.R
ape/R/corphylo.R
ape/R/dist.gene.R
ape/R/cophenetic.phylo.R
ape/R/makeNodeLabel.R
ape/R/diversi.gof.R
ape/R/treePop.R
ape/R/lmorigin.R
ape/R/MPR.R
ape/R/CADM.global.R
ape/R/speciesTree.R
ape/R/read.tree.R
ape/R/drop.tip.R
ape/R/read.gff.R
ape/R/ewLasso.R
ape/R/DNA.R
ape/R/identify.phylo.R
ape/R/binaryPGLMM.R
ape/R/delta.plot.R
ape/R/vcv2phylo.R
ape/R/mrca.R
ape/R/node.dating.R
ape/R/write.nexus.data.R
ape/R/compar.gee.R
ape/R/cherry.R
ape/R/as.phylo.formula.R
ape/R/howmanytrees.R
ape/R/as.phylo.R
ape/R/summary.phylo.R
ape/R/birthdeath.R
ape/R/subtreeplot.R
ape/R/nodepath.R
ape/R/all.equal.phylo.R
ape/R/which.edge.R
ape/R/MoranI.R
ape/R/evonet.R
ape/R/nj.R
ape/R/is.compatible.R
ape/R/mvr.R
ape/R/rTrait.R
ape/R/ltt.plot.R
ape/R/collapsed.intervals.R
ape/R/rotate.R
ape/R/extract.popsize.R
ape/R/skyline.R
ape/R/makeLabel.R
ape/R/matexpo.R
ape/R/parafit.R
ape/R/pcoa.R
ape/R/write.nexus.R
ape/R/print.parafit.R
ape/R/yule.R
ape/R/as.bitsplits.R
ape/R/mst.R
ape/R/checkValidPhylo.R
ape/R/yule.time.R
ape/R/branching.times.R
ape/R/compar.ou.R
ape/R/plot.popsize.R
ape/R/clustal.R
ape/R/root.R
ape/R/write.dna.R
ape/R/collapse.singles.R
ape/R/read.GenBank.R
ape/R/triangMtd.R
ape/R/rtt.R
ape/R/pic.R
ape/R/CADM.post.R
ape/R/print.lmorigin.R
ape/R/reconstruct.R
ape/R/ladderize.R
ape/R/subtrees.R
ape/R/mcmc.popsize.R
ape/R/bind.tree.R
ape/R/chronoMPL.R
ape/R/is.ultrametric.R
ape/R/read.nexus.R
ape/R/nodelabels.R
ape/R/vcv.phylo.R
ape/R/phydataplot.R
ape/R/varcomp.R
ape/R/chronos.R
ape/R/mantel.test.R
ape/R/multi2di.R
ape/R/unique.multiPhylo.R
ape/R/plot.phyloExtra.R
ape/R/additive.R
ape/R/coalescent.intervals.R
ape/R/alex.R
ape/R/plotPhyloCoor.R
ape/R/PGLS.R
ape/R/diversi.time.R
ape/R/njs.R
ape/R/dist.topo.R
ape/R/write.tree.R
ape/R/as.matching.R
ape/R/SDM.R
ape/R/SlowinskiGuyer.R
ape/R/zzz.R
ape/R/scales.R
ape/R/reorder.phylo.R
ape/R/read.caic.R
ape/vignettes
ape/vignettes/ape.bib
ape/vignettes/MoranI.Rnw
ape/MD5
ape/build
ape/build/vignette.rds
ape/DESCRIPTION
ape/man
ape/man/makeLabel.Rd
ape/man/bd.ext.Rd
ape/man/makeNodeLabel.Rd
ape/man/read.dna.Rd
ape/man/mcconwaysims.test.Rd
ape/man/binaryPGLMM.Rd
ape/man/compute.brlen.Rd
ape/man/ewLasso.Rd
ape/man/pic.ortho.Rd
ape/man/plot.correlogram.Rd
ape/man/add.scale.bar.Rd
ape/man/richness.yule.test.Rd
ape/man/multi2di.Rd
ape/man/trex.Rd
ape/man/mantel.test.Rd
ape/man/edges.Rd
ape/man/rTraitDisc.Rd
ape/man/varcomp.Rd
ape/man/mat5Mrand.Rd
ape/man/nodelabels.Rd
ape/man/checkAlignment.Rd
ape/man/varCompPhylip.Rd
ape/man/compar.gee.Rd
ape/man/del.gaps.Rd
ape/man/pic.Rd
ape/man/where.Rd
ape/man/unique.multiPhylo.Rd
ape/man/is.compatible.Rd
ape/man/SDM.Rd
ape/man/bird.orders.Rd
ape/man/plot.phyloExtra.Rd
ape/man/triangMtd.Rd
ape/man/ape-package.Rd
ape/man/MoranI.Rd
ape/man/chronoMPL.Rd
ape/man/AAbin.Rd
ape/man/howmanytrees.Rd
ape/man/cophyloplot.Rd
ape/man/dbd.Rd
ape/man/chronopl.Rd
ape/man/read.GenBank.Rd
ape/man/LTT.Rd
ape/man/c.phylo.Rd
ape/man/DNAbin.Rd
ape/man/hivtree.Rd
ape/man/as.bitsplits.Rd
ape/man/corBlomberg.Rd
ape/man/mat3.Rd
ape/man/dist.dna.Rd
ape/man/compar.lynch.Rd
ape/man/stree.Rd
ape/man/read.tree.Rd
ape/man/weight.taxo.Rd
ape/man/subtrees.Rd
ape/man/reorder.phylo.Rd
ape/man/kronoviz.Rd
ape/man/read.nexus.Rd
ape/man/def.Rd
ape/man/rtt.Rd
ape/man/phymltest.Rd
ape/man/yule.cov.Rd
ape/man/speciesTree.Rd
ape/man/boot.phylo.Rd
ape/man/rTraitMult.Rd
ape/man/rotate.Rd
ape/man/skyline.Rd
ape/man/skylineplot.Rd
ape/man/is.monophyletic.Rd
ape/man/all.equal.phylo.Rd
ape/man/axisPhylo.Rd
ape/man/corPagel.Rd
ape/man/print.phylo.Rd
ape/man/plot.varcomp.Rd
ape/man/dist.gene.Rd
ape/man/write.dna.Rd
ape/man/compute.brtime.Rd
ape/man/is.binary.tree.Rd
ape/man/branching.times.Rd
ape/man/additive.Rd
ape/man/corClasses.Rd
ape/man/bind.tree.Rd
ape/man/bird.families.Rd
ape/man/alex.Rd
ape/man/corBrownian.Rd
ape/man/rTraitCont.Rd
ape/man/is.ultrametric.Rd
ape/man/chronos.Rd
ape/man/compar.cheverud.Rd
ape/man/MPR.Rd
ape/man/mat5M3ID.Rd
ape/man/as.matching.Rd
ape/man/correlogram.formula.Rd
ape/man/njs.Rd
ape/man/write.tree.Rd
ape/man/root.Rd
ape/man/bd.time.Rd
ape/man/corphylo.Rd
ape/man/birthdeath.Rd
ape/man/compar.ou.Rd
ape/man/multiphylo.Rd
ape/man/summary.phylo.Rd
ape/man/alview.Rd
ape/man/diversi.gof.Rd
ape/man/mvr.Rd
ape/man/consensus.Rd
ape/man/matexpo.Rd
ape/man/diversi.time.Rd
ape/man/as.alignment.Rd
ape/man/which.edge.Rd
ape/man/rtree.Rd
ape/man/identify.phylo.Rd
ape/man/mixedFontLabel.Rd
ape/man/zoom.Rd
ape/man/corGrafen.Rd
ape/man/DNAbin2indel.Rd
ape/man/trans.Rd
ape/man/write.nexus.data.Rd
ape/man/carnivora.Rd
ape/man/vcv.phylo.Rd
ape/man/subtreeplot.Rd
ape/man/node.dating.Rd
ape/man/corMartins.Rd
ape/man/clustal.Rd
ape/man/read.gff.Rd
ape/man/nj.Rd
ape/man/node.depth.Rd
ape/man/vcv2phylo.Rd
ape/man/phydataplot.Rd
ape/man/rlineage.Rd
ape/man/yule.Rd
ape/man/write.nexus.Rd
ape/man/Initialize.corPhyl.Rd
ape/man/evonet.Rd
ape/man/yule.time.Rd
ape/man/diversity.contrast.test.Rd
ape/man/slowinskiguyer.test.Rd
ape/man/chiroptera.Rd
ape/man/as.phylo.Rd
ape/man/lmorigin.Rd
ape/man/ltt.plot.Rd
ape/man/dist.topo.Rd
ape/man/bionj.Rd
ape/man/read.caic.Rd
ape/man/image.DNAbin.Rd
ape/man/reconstruct.Rd
ape/man/mst.Rd
ape/man/treePop.Rd
ape/man/all.equal.DNAbin.Rd
ape/man/fastme.Rd
ape/man/collapsed.intervals.Rd
ape/man/mrca.Rd
ape/man/as.phylo.formula.Rd
ape/man/read.nexus.data.Rd
ape/man/nodepath.Rd
ape/man/collapse.singles.Rd
ape/man/balance.Rd
ape/man/woodmouse.Rd
ape/man/ladderize.Rd
ape/man/cherry.Rd
ape/man/CADM.global.Rd
ape/man/base.freq.Rd
ape/man/delta.plot.Rd
ape/man/ace.Rd
ape/man/parafit.Rd
ape/man/plotTreeTime.Rd
ape/man/pcoa.Rd
ape/man/seg.sites.Rd
ape/man/cynipids.Rd
ape/man/gammaStat.Rd
ape/man/cophenetic.phylo.Rd
ape/man/ape-internal.Rd
ape/man/plot.phylo.Rd
ape/man/drop.tip.Rd
ape/man/coalescent.intervals.Rd
ape/man/checkValidPhylo.Rd
ape/man/mcmc.popsize.Rd
ape/man/label2table.Rd