CRAN/E | ape

ape

Analyses of Phylogenetics and Evolution

Installation

About

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.

Citation ape citation info
ape-package.ird.fr/
github.com/emmanuelparadis/ape
Bug report File report

Key Metrics

Version 5.7-1
R ≥ 3.2.0
Published 2023-03-13 381 days ago
Needs compilation? yes
License GPL-2
License GPL-3
CRAN checks ape results

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Maintainer

Maintainer

Emmanuel Paradis

Emmanuel.Paradis@ird.fr

Authors

Emmanuel Paradis

aut / cre / cph

Simon Blomberg

aut / cph

Ben Bolker

aut / cph

Joseph Brown

aut / cph

Santiago Claramunt

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

RJ Ewing

aut / cph

Olivier Gascuel

aut / cph

Thomas Guillerme

aut / cph

Christoph Heibl

aut / cph

Anthony Ives

aut / cph

Bradley Jones

aut / cph

Franz Krah

aut / cph

Daniel Lawson

aut / cph

Vincent Lefort

aut / cph

Pierre Legendre

aut / cph

Jim Lemon

aut / cph

Guillaume Louvel

aut / cph

Eric Marcon

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

Material

README
NEWS
Reference manual
Package source

In Views

Environmetrics
Phylogenetics

Vignettes

Drawing Phylogenies
Moran's I
Random Topology

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

ape archive

Depends

R ≥ 3.2.0

Imports

nlme
lattice
graphics
methods
stats
utils
parallel
Rcpp ≥ 0.12.0
digest

Suggests

gee
expm
igraph
phangorn

LinkingTo

Rcpp

Reverse Depends

Anaconda
apex
aphylo
apTreeshape
BAMMtools
BarcodingR
BDMMAcorrect
Canopy
caper
cati
Claddis
clstutils
coalescentMCMC
CommEcol
convevol
corHMM
ctpm
dispRity
distory
diversitree
FD
geiger
hisse
ips
jrich
MCMCglmm
MCMCtreeR
MiSPU
MonoPhy
motmot
MPSEM
MSCquartets
MSCsimtester
mvMORPH
nichevol
nodeSub
OUwie
paleotree
pegas
perspectev
pez
phangorn
phyclust
phyloclim
PhylogeneticEM
phylolm
phylotools
phyloTop
phytools
picante
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(warning: might lead to performance issues and take some time)

Reverse Imports

abdiv
adaptiveGPCA
adegenet
adephylo
adiv
alakazam
animalcules
AnnotationBustR
aPCoA
arakno
autoGO
BAT
BayesSPsurv
beastier
beautier
betapart
BIEN
bioseq
bite
bnpsd
BoSSA
CALANGO
canaper
ccfindR
chemodiv
CluMSID
clusterExperiment
coil
colordistance
compcodeR
concatipede
copyseparator
covid19.analytics
CRABS
DAMOCLES
dartR
DCLEAR
DDD
debar
DHARMa
DIAlignR
dowser
ecospat
entropart
EnvNJ
EpiModel
epm
evobiR
evolvability
EvoPhylo
Load all 225 items
(warning: might lead to performance issues and take some time)

Reverse Suggests

ACDC
ade4
adespatial
aphid
aqp
asnipe
babette
brms
changeRangeR
CongreveLamsdell2016
CTNote
data.tree
dcGOR
deeptime
dendextend
dynamicSDM
ecolottery
enveomics.R
fido
FinePop
gamclass
ggimage
ggmsa
GLSME
hagis
harmonicmeanp
hierfstat
HSAUR
HSAUR2
HSAUR3
idpr
igraph
kmer
lingtypology
mcbette
mdendro
meconetcomp
mecoturn
metadat
metafor
metagear
msa
MVA
netdiffuseR
nosoi
occCite
OptCirClust
orthogene
ouch
outbreaks
Load all 83 items
(warning: might lead to performance issues and take some time)

Reverse Enhances

clue