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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 21 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

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