Other packages > Find by keyword >

phytools  

Phylogenetic Tools for Comparative Biology (and Other Things)
View on CRAN: Click here


Download and install phytools package within the R console
Install from CRAN:
install.packages("phytools")

Install from Github:
library("remotes")
install_github("cran/phytools")

Install by package version:
library("remotes")
install_version("phytools", "2.5-2")



Attach the package and use:
library("phytools")
Maintained by
Liam J. Revell
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2011-08-20
Latest Update: 2025-01-08
Description:
A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.
How to cite:
Liam J. Revell (2011). phytools: Phylogenetic Tools for Comparative Biology (and Other Things). R package version 2.5-2, https://cran.r-project.org/web/packages/phytools. Accessed 05 Jun. 2026.
Previous versions and publish date:
0.0-8 (2011-08-20 06:57), 0.1-0 (2011-10-17 07:55), 0.1-2 (2011-11-27 10:14), 0.1-5 (2011-12-18 10:10), 0.1-6 (2012-01-11 08:02), 0.1-7 (2012-02-27 08:35), 0.1-8 (2012-05-02 08:28), 0.1-9 (2012-08-08 23:31), 0.2-0 (2012-09-29 23:10), 0.2-1 (2012-11-13 08:09), 0.2-20 (2013-02-17 14:11), 0.2-30 (2013-03-20 19:14), 0.2-40 (2013-04-08 07:20), 0.2-50 (2013-04-20 23:18), 0.2-70 (2013-05-22 21:44), 0.2-80 (2013-05-31 15:21), 0.2-90 (2013-06-30 01:38), 0.3-10 (2013-07-16 16:08), 0.3-72.1 (2014-03-03 09:44), 0.3-72 (2013-10-25 07:29), 0.3-93 (2014-03-03 22:45), 0.4-05 (2014-05-05 07:16), 0.4-21 (2014-06-28 19:31), 0.4-31 (2014-08-26 22:47), 0.4-45 (2015-02-05 22:04), 0.4-56 (2015-04-29 08:41), 0.4-60 (2015-07-10 20:33), 0.5-00 (2015-09-25 09:02), 0.5-10 (2015-12-10 09:57), 0.5-20 (2016-03-06 23:34), 0.5-38 (2016-06-24 07:30), 0.5-64 (2016-12-05 22:45), 0.6-00 (2017-03-28 23:11), 0.6-20 (2017-07-28 07:53), 0.6-44 (2017-11-12 16:13), 0.6-60 (2018-09-28 06:50), 0.6-99 (2019-06-18 14:50), 0.7-20 (2020-03-19 15:20), 0.7-47 (2020-06-01 23:00), 0.7-70 (2020-09-20 00:20), 0.7-80 (2021-06-03 13:10), 0.7-90 (2021-09-25 22:50), 1.0-1 (2022-01-03 14:50), 1.0-3 (2022-04-05 22:20), 1.2-0 (2022-09-01 19:30), 1.5-1 (2023-02-19 14:20), 1.9-16 (2023-07-14 22:00), 2.0-3 (2023-11-09 23:40), 2.1-1 (2024-01-09 11:00), 2.3-0 (2024-06-14 00:50), 2.4-4 (2025-01-08 01:30)
Other packages that cited phytools R package
View phytools citation profile
Other R packages that phytools depends, imports, suggests or enhances
Complete documentation for phytools
Functions, R codes and Examples using the phytools R package
Some associated functions: Dtest . add.arrow . add.color.bar . add.everywhere . add.random . add.simmap.legend . add.species.to.genus . aic.w . allFurcTrees . anc.Bayes . anc.ML . anc.trend . ancThresh . ancr . anoletree . ansi_phylo . applyBranchLengths . as.Qmatrix . as.multiPhylo . ave.rates . averageTree . bd . bind.tip . bind.tree.simmap . bmPlot . branching.diffusion . brownie.lite . brownieREML . cladelabels . collapse.to.star . collapseTree . compare.chronograms . consensus.edges . contMap . cophylo . cospeciation . countSimmap . ctt . density.multiSimmap . densityMap . densityTree . describe.simmap . di2multi.simmap . dotTree . drop.clade . drop.leaves . drop.tip.contMap . drop.tip.multiSimmap . drop.tip.simmap . edge.widthMap . edgeProbs . estDiversity . evol.rate.mcmc . evol.vcv . evolvcv.lite . exhaustiveMP . expand.clade . export.as.xml . fancyTree . fastAnc . fastBM . fastMRCA . findMRCA . fit.bd . fitBayes . fitDiversityModel . fitMk . fitPagel . force.ultrametric . gamma_pruning . gammatest . genSeq . geo.legend . get.treepos . getCladesofSize . getDescendants . getExtant . getSisters . getStates . labelnodes . ladderize.simmap . lambda.transform . likMlambda . linklabels . locate.fossil . locate.yeti . ls.tree . ltt . ltt95 . make.era.map . make.simmap . map.overlap . map.to.singleton . mapped.states . markChanges . matchNodes . mergeMappedStates . midpoint.root . minRotate . minSplit . modified.Grafen . mrp.supertree . multi.mantel . multiC . multiRF . multirateBM . nodeHeights . nodelabels.cophylo . optim.phylo.ls . orderMappedEdge . paintSubTree . paste.tree . pbtree . pgls.Ives . phenogram . phyl.RMA . phyl.cca . phyl.pairedttest . phyl.pca . phyl.resid . phyl.vcv . phylANOVA . phylo.heatmap . phylo.impute . phylo.to.map . phylo.toBackbone . phyloDesign . phylomorphospace . phylomorphospace3d . phylosig . phytools-package . plot.backbonePhylo . plotBranchbyTrait . plotSimmap . plotThresh . plotTree.datamatrix . plotTree.errorbars . plotTree . plotTree.wBars . posterior.evolrate . posthoc . print.backbonePhylo . pscore . ratebystate . ratebytree . rateshift . read.newick . read.simmap . reorder.backbonePhylo . reorderSimmap . rep.phylo . reroot . rerootingMethod . rescale . rescaleSimmap . resolveNode . rotateNodes . roundBranches . roundPhylogram . rstate . sampleFrom . setMap . sim.corrs . sim.history . sim.ratebystate . sim.rates . simBMphylo . skewers . splitEdgeColor . splitTree . splitplotTree . starTree . strahlerNumber . threshBayes . threshDIC . threshState . to.matrix . tree.grow . treeSlice . untangle . vcvPhylo . write.simmap . writeAncestors . writeNexus . 
Some associated R codes: Dtest.R . add.everywhere.R . add.random.R . add.species.to.genus.R . allFurcTrees.R . anc.Bayes.R . anc.ML.R . anc.trend.R . ancThresh.R . ansi_phylo.R . asr.R . backbonePhylo.R . bd.R . bmPlot.R . branching.diffusion.R . brownie.lite.R . brownieREML.R . collapseTree.R . compare.chronograms.R . consensus.edges.R . contMap.R . cophylo.R . cospeciation.R . cotangleplot.R . ctt.R . densityMap.R . densityTree.R . dotTree.R . drop.tip.simmap.R . estDiversity.R . evol.rate.mcmc.R . evol.vcv.R . evolvcv.lite.R . exhaustiveMP.R . export.as.xml.R . fancyTree.R . fastAnc.R . fastBM.R . fitBayes.R . fitBiogeog.R . fitDiversityModel.R . fitHRM.R . fitMk.R . fitMk.parallel.R . fitPagel.R . fitgammaMk.R . fitmultiMk.R . fitpolyMk.R . locate.fossil.R . locate.yeti.R . ls.consensus.R . ltt.R . ltt95.R . make.era.map.R . make.simmap.R . map.overlap.R . map.to.singleton.R . mcmcBM.R . mcmcBM.full.R . mcmcLambda.R . mcmcMk.R . mrp.supertree.R . multi.mantel.R . multiRF.R . multirateBM.R . optim.phylo.ls.R . paintSubTree.R . parsimony.R . pbtree.R . pgls.Ives.R . phenogram.R . phyl.RMA.R . phyl.cca.R . phyl.pairedttest.R . phyl.pca.R . phyl.resid.R . phylANOVA.R . phylo.heatmap.R . phylo.impute.R . phylo.to.map.R . phylomorphospace.R . phylomorphospace3d.R . phylosig.R . plotBranchbyTrait.R . plotSimmap.R . plotTree.datamatrix.R . plotTree.errorbars.R . plotTree.wBars.R . plotrix_fn.R . project.phylomorphospace.R . ratebystate.R . ratebytree.R . rateshift.R . read.newick.R . read.simmap.R . readNexus.R . rerootingMethod.R . resolveNodes.R . roundPhylogram.R . sim.corrs.R . sim.history.R . sim.rates.R . simBMphylo.R . skewers.R . splitplotTree.R . starTree.R . strahlerNumber.R . threshBayes.R . tree.grow.R . treeSlice.R . utilities.R . write.simmap.R . writeAncestors.R . writeNexus.R .  Full phytools package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

crossurr  
Cross-Fitting for Doubly Robust Evaluation of High-Dimensional Surrogate Markers
Doubly robust methods for evaluating surrogate markers as outlined in: Agniel D, Hejblum BP, Thiebau ...
Download / Learn more Package Citations See dependency  
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  
ibb  
R Wrapper for Istanbul Municipality Open Data Portal
Call wrappers for Istanbul Metropolitan Municipality's Open Data Portal (Turkish: Istanbul B ...
Download / Learn more Package Citations See dependency  
msm  
Multi-State Markov and Hidden Markov Models in Continuous Time
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal d ...
Download / Learn more Package Citations See dependency  
envirem  
Generation of ENVIREM Variables
Generation of bioclimatic rasters that are complementary to the typical 19 bioclim variables. ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA