R package citation, R package reverse dependencies, R package scholars, install an r package from GitHub hy is package acceptance pending why is package undeliverable amazon why is package on hold dhl tour packages why in r package r and r package full form why is r free why r is bad which r package to install which r package has which r package which r package version which r package readxl which r package ggplot which r package fread which r package license where is package.json where is package-lock.json where is package.swift where is package explorer in eclipse where is package where is package manager unity where is package installer android where is package manager console in visual studio who r package which r package to install which r package version who is package who is package deal who is package design r and r package full form r and r package meaning what r package has what package r what is package in java what is package what is package-lock.json what is package in python what is package.json what is package installer do r package can't install r packages r can't find package r can't load package can't load xlsx package r can't install psych package r can't install sf package r Write if else in NONMEM pk pd
ape
Analyses of Phylogenetics and Evolution
View on CRAN: Click
here
Download and install ape package within the R console
Install from CRAN:
install.packages("ape")
Install from Github:
library("remotes")
install_github("cran/ape") Install by package version:
library("remotes")
install_version("ape", "5.8-1") Attach the package and use:
library("ape")
Maintained by
Emmanuel Paradis
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2002-08-31
Latest Update: 2024-12-16
Description:
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.
How to cite:
Emmanuel Paradis (2002). ape: Analyses of Phylogenetics and Evolution. R package version 5.8-1, https://cran.r-project.org/web/packages/ape. Accessed 16 Jul. 2026.
Previous versions and publish date:
(2026-07-09 07:18), 0.1 (2002-08-31 10:58), 0.2-1 (2002-10-28 22:33), 0.2 (2002-10-04 12:36), 1.0 (2003-03-04 18:08), 1.1-1 (2003-06-06 17:04), 1.1-2 (2003-07-15 20:32), 1.1-3 (2003-09-05 08:04), 1.1 (2003-06-03 20:38), 1.2-1 (2004-02-04 17:04), 1.2-2 (2004-03-19 23:27), 1.2-3 (2004-05-24 22:01), 1.2-4 (2004-08-07 11:13), 1.2-5 (2004-08-24 12:32), 1.2-6 (2004-09-17 10:37), 1.2-7 (2004-09-29 15:03), 1.2 (2004-01-07 08:33), 1.3-1 (2004-11-12 13:14), 1.3 (2004-11-04 16:41), 1.4 (2004-12-23 16:17), 1.5 (2005-04-19 10:17), 1.6 (2005-06-03 13:04), 1.7 (2005-09-19 12:53), 1.8-1 (2006-02-17 17:37), 1.8-2 (2006-03-24 10:14), 1.8-3 (2006-06-06 15:59), 1.8-4 (2006-07-24 10:24), 1.8-5 (2006-09-18 21:50), 1.8 (2005-12-19 12:07), 1.9-1 (2006-12-14 12:06), 1.9-2 (2007-01-24 12:06), 1.9-3 (2007-02-28 09:56), 1.9-4 (2007-03-27 21:04), 1.9 (2006-11-20 09:21), 1.10-1 (2007-06-19 13:47), 1.10-2 (2007-07-07 20:51), 1.10 (2007-05-01 21:04), 2.0-1 (2007-09-07 15:49), 2.0-2 (2007-11-17 11:43), 2.0 (2007-09-07 13:15), 2.1-1 (2008-02-01 23:13), 2.1-2 (2008-02-29 17:53), 2.1-3 (2008-03-21 20:26), 2.1 (2008-01-04 16:48), 2.2-1 (2008-07-11 19:21), 2.2-2 (2008-10-09 20:58), 2.2-3 (2009-01-13 11:32), 2.2-4 (2009-02-09 12:32), 2.2 (2008-05-08 09:13), 2.3-1 (2009-06-23 16:00), 2.3-2 (2009-07-21 14:27), 2.3-3 (2009-09-22 17:01), 2.3 (2009-03-30 08:56), 2.4-1 (2009-11-23 20:19), 2.4 (2009-10-05 17:02), 2.5-1 (2010-04-06 19:12), 2.5-2 (2010-05-17 11:09), 2.5-3 (2010-06-15 10:50), 2.5 (2010-02-02 11:09), 2.6-1 (2010-11-03 08:40), 2.6-2 (2010-12-08 10:28), 2.6-3 (2011-02-18 18:29), 2.6 (2010-09-30 07:41), 2.7-1 (2011-03-26 17:04), 2.7-2 (2011-06-17 08:44), 2.7-3 (2011-08-09 06:59), 2.7 (2011-03-17 06:45), 2.8 (2011-10-24 16:40), 3.0-1 (2012-02-20 10:24), 3.0-2 (2012-04-05 07:54), 3.0-3 (2012-04-24 17:08), 3.0-4 (2012-08-01 11:03), 3.0-5 (2012-10-08 18:49), 3.0-6 (2013-01-18 20:22), 3.0-7 (2013-01-21 14:52), 3.0-8 (2013-04-02 12:35), 3.0-9 (2013-07-19 16:25), 3.0-10 (2013-09-10 08:01), 3.0-11 (2013-10-01 11:19), 3.0 (2012-02-10 09:36), 3.1-1 (2014-03-11 08:49), 3.1-2 (2014-05-27 12:44), 3.1-3 (2014-07-12 15:03), 3.1-4 (2014-07-15 11:13), 3.1 (2014-03-05 10:02), 3.2 (2014-12-05 17:18), 3.3 (2015-05-29 12:44), 3.4 (2015-11-29 19:14), 3.5 (2016-05-24 05:39), 4.0 (2016-12-01 17:40), 4.1 (2017-02-14 19:15), 5.0 (2017-10-30 16:36), 5.1 (2018-04-05 00:16), 5.2 (2018-09-24 10:00), 5.3 (2019-03-17 08:15), 5.4-1 (2020-08-13 07:20), 5.4 (2020-06-03 14:20), 5.5 (2021-04-25 10:20), 5.6-1 (2022-01-07 15:32), 5.6-2 (2022-03-02 13:30), 5.6 (2021-12-21 10:20), 5.7-1 (2023-03-13 13:20), 5.7 (2023-02-16 14:30), 5.8 (2024-04-11 14:30)
Other packages that cited ape R package
View ape citation profile
Other R packages that ape depends,
imports, suggests or enhances
Complete documentation for ape
Functions, R codes and Examples using
the ape R package
Some associated functions: AAbin . CADM.global . DNAbin . DNAbin2indel . Initialize.corPhyl . LTT . MPR . MoranI . SDM . ace . add.scale.bar . additive . alex . all.equal.DNAbin . all.equal.phylo . alview . ape-internal . ape-package . apetools . as.alignment . as.bitsplits . as.matching . as.phylo.formula . as.phylo . axisPhylo . balance . base.freq . bd.ext . bd.time . binaryPGLMM . bind.tree . bionj . bird.families . bird.orders . birthdeath . boot.phylo . branching.times . c.phylo . carnivora . checkAlignment . checkLabel . checkValidPhylo . cherry . chiroptera . chronoMPL . chronopl . chronos . clustal . coalescent.intervals . collapse.singles . collapsed.intervals . compar.cheverud . compar.gee . compar.lynch . compar.ou . comparePhylo . compute.brlen . compute.brtime . consensus . cophenetic.phylo . cophyloplot . corBlomberg . corBrownian . corClasses . corGrafen . corMartins . corPagel . corphylo . correlogram.formula . cynipids . dbd . def . degree . del.gaps . delta.plot . dist.dna . dist.gene . dist.topo . diversi.gof . diversi.time . diversity.contrast.test . dnds . drop.tip . edges . evonet . ewLasso . fastme . gammaStat . getAnnotationsGenBank . hivtree . howmanytrees . identify.phylo . image.DNAbin . is.binary.tree . is.compatible . is.monophyletic . is.ultrametric . kronoviz . label2table . ladderize . latag2n . lmorigin . ltt.plot . makeLabel . makeNodeLabel . mantel.test . mat3 . mat5M3ID . mat5Mrand . matexpo . mcconwaysims.test . mcmc.popsize . mixedFontLabel . mrca . mst . multi2di . multiphylo . mvr . nj . njs . node.dating . node.depth . nodelabels . nodepath . parafit . pcoa . phydataplot . phymltest . pic . pic.ortho . plot.correlogram . plot.phylo . plot.phyloExtra . plot.varcomp . plotTreeTime . print.phylo . rDNAbin . rTraitCont . rTraitDisc . rTraitMult . read.GenBank . read.caic . read.dna . read.gff . read.nexus.data . read.nexus . read.tree . reconstruct . reorder.phylo . richness.yule.test . rlineage . root . rotate . rtree . rtt . seg.sites . skyline . skylineplot . slowinskiguyer.test . solveAmbiguousBases . speciesTree . stree . subtreeplot . subtrees . summary.phylo . trans . treePop . trex . triangMtd . unique.multiPhylo . updateLabel . varCompPhylip . varcomp . vcv.phylo . vcv2phylo . weight.taxo . where . which.edge . woodmouse . write.dna . write.nexus.data . write.nexus . write.tree . yule.cov . yule . yule.time . zoom .
Some associated R codes: CADM.global.R . CADM.post.R . CDF.birth.death.R . Cheverud.R . DNA.R . MPR.R . MoranI.R . PGLS.R . RcppExports.R . SDM.R . SlowinskiGuyer.R . ace.R . additive.R . alex.R . all.equal.phylo.R . apetools.R . as.bitsplits.R . as.matching.R . as.phylo.R . as.phylo.formula.R . balance.R . binaryPGLMM.R . bind.tree.R . biplot.pcoa.R . birthdeath.R . branching.times.R . checkValidPhylo.R . cherry.R . chronoMPL.R . chronopl.R . chronos.R . clustal.R . coalescent.intervals.R . collapse.singles.R . collapsed.intervals.R . compar.gee.R . compar.lynch.R . compar.ou.R . comparePhylo.R . compute.brtime.R . cophenetic.phylo.R . cophyloplot.R . corphylo.R . dbd.R . def.R . delta.plot.R . dist.gene.R . dist.topo.R . diversi.gof.R . diversi.time.R . drop.tip.R . evonet.R . ewLasso.R . extract.popsize.R . gammaStat.R . howmanytrees.R . identify.phylo.R . is.binary.tree.R . is.compatible.R . is.monophyletic.R . is.ultrametric.R . ladderize.R . lmorigin.R . ltt.plot.R . makeLabel.R . makeNodeLabel.R . mantel.test.R . matexpo.R . mcmc.popsize.R . me.R . mrca.R . mst.R . multi2di.R . mvr.R . nj.R . njs.R . node.dating.R . nodelabels.R . nodepath.R . parafit.R . pcoa.R . phydataplot.R . phymltest.R . pic.R . plot.phylo.R . plot.phyloExtra.R . plot.popsize.R . plotPhyloCoor.R . print.lmorigin.R . print.parafit.R . rTrait.R . read.GenBank.R . read.caic.R . read.dna.R . read.gff.R . read.nexus.R . read.nexus.data.R . read.tree.R . reconstruct.R . reorder.phylo.R . root.R . rotate.R . rtree.R . rtt.R . scales.R . skyline.R . skylineplot.R . speciesTree.R . subtreeplot.R . subtrees.R . summary.phylo.R . treePop.R . triangMtd.R . unique.multiPhylo.R . varcomp.R . vcv.phylo.R . vcv2phylo.R . which.edge.R . write.dna.R . write.nexus.R . write.nexus.data.R . write.tree.R . yule.R . yule.time.R . zoom.R . zzz.R . Full ape package functions and examples
Downloads during the last 30 days
Today's Hot Picks in Authors and Packages
stevedata
Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics
This is a collection of various kinds of data with broad uses for teaching. My students, and academ ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Steve Miller (view profile)
schoolmath
Functions and Datasets for Math Used in School
Contains functions and datasets for math taught in school. A main focus is set to prime-calculation. ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Jörg große Schlarmann (view profile)
bbdetection
Identification of Bull and Bear States of the Market
Implements two algorithms of detecting Bull and Bear markets in stock prices: the algorithm of Pagan ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Valeriy Zakamulin (view profile)
tibble
Simple Data Frames
Provides a 'tbl_df' class (the 'tibble') with stricter checking and better formatting than the tradi ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Kirill Müller (view profile)
nextGenShinyApps
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Obinna Obianom (view profile)
Rnmr1D
Perform the Complete Processing of a Set of Proton Nuclear Magnetic Resonance Spectra
Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Daniel Jacob (view profile)
27,806
R Packages
239,283
Dependencies
73,837
Author Associations
27,807
Publication Badges
