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 22 Dec. 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), 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

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

elect

Estimation of Life Expectancies Using Multi-State Models

Functions to compute state-specific and marginal life expectancies. The computation is based on a fi ...
Download / Learn more Package Citations See dependency

Maintainer: Ardo van den Hout (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)

composits

Compositional, Multivariate and Univariate Time Series Outlier Ensemble

A compositional multivariate and univariate time series outlier ensemble.It uses the four R packages ...
Download / Learn more Package Citations See dependency

Maintainer: Sevvandi Kandanaarachchi (view profile)

tropAlgebra

Tropical Algebraic Functions

It includes functions like tropical addition, tropical multiplication for vectors and matrices. In t ...
Download / Learn more Package Citations See dependency

Maintainer: Muhammad Kashif Hanif (view profile)

LOGANTree

Tree-Based Models for the Analysis of Log Files from Computer-Based Assessments

Enables researchers to model log-file data from computer-based assessments using machine-learning te ...
Download / Learn more Package Citations See dependency

Maintainer: Qi Qin (view profile)

dmlalg

Double Machine Learning Algorithms

Implementation of double machine learning (DML) algorithms in R, based on Emmenegger and Buehlmann ...
Download / Learn more Package Citations See dependency

Maintainer: Corinne Emmenegger (view profile)