Other packages > Find by keyword >

Explore topics

By keyword . Oldest R packages . Newest R packages . Top downloaded R packages . Datasets . Archived R packages . Top downloaded last week . Top downloaded yesterday

ape

Star Watch Copy Code

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")

Attach the package and use:

 library("ape")

Maintained by
Emmanuel Paradis
[Scholar Profile | Author Map]

All associated links for this package

First Published: 2002-08-31

Latest Update: 2023-03-13

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, https://cran.r-project.org/web/packages/ape. Accessed 06 Nov. 2024.

Previous versions and publish date:

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)

Other packages that cited ape R package

View ape citation profile

Other R packages that ape depends, imports, suggests or enhances

View ape dependency map

Complete documentation for ape

View documentation PDF

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

Get rewarded with contribution points by helping add

Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

mailR

A Utility to Send Emails from R

Interface to Apache Commons Email to send emails from R. ...
Download / Learn more Package Citations See dependency

Maintainer: Rahul Premraj (view profile)

maic

Matching-Adjusted Indirect Comparison

A generalised workflow for generation of subject weights to be used in Matching-Adjusted Indirect C ...
Download / Learn more Package Citations See dependency

Maintainer: Rob Young (view profile)

equatiomatic

Transform Models into 'LaTeX' Equations

The goal of equatiomatic is to reduce the painassociated with writing LaTeX formulas from fitted mod ...
Download / Learn more Package Citations See dependency

Maintainer: Philippe Grosjean (view profile)

memoise

'Memoisation' of Functions

Cache the results of a function so that when you call it again with the same arguments it returns t ...
Download / Learn more Package Citations See dependency

Maintainer: Winston Chang (view profile)

quickcode

Quick and Essential 'R' Tricks for Better Scripts

The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency

Maintainer: Obinna Obianom (view profile)

ddp

Desirable Dietary Pattern

The desirable Dietary Pattern (DDP)/ PPH score measures the variety of food consumption. The (weigh ...
Download / Learn more Package Citations See dependency

Maintainer: Weksi Budiaji (view profile)