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
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]
[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 15 Jul. 2026.
Previous versions and publish date:
(2026-07-09 06:41), 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
SECFISH
Disaggregate Variable Costs
These functions were developed within SECFISH project (Strengthening regional cooperation in the are ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Isabella Bitetto (view profile)
pulseTD
Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data
A tool for analyzing the transcription, processing and degradation rates of genes by 4sU-seq (the Me ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: XinWang (view profile)
binhf
Haar-Fisz Functions for Binomial Data
Binomial Haar-Fisz transforms for Gaussianization as in Nunes and Nason (2009). ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Matt Nunes (view profile)
gscaLCA
Generalized Structure Component Analysis- Latent Class Analysis & Latent Class Regression
Execute Latent Class Analysis (LCA) and Latent Class Regression (LCR) by using Generalized Structu ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Seohee Park (view profile)
footBayes
Fitting Bayesian and MLE Football Models
This is the first package allowing for the estimation,
visualization and prediction of the most wel ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Leonardo Egidi (view profile)
PermAlgo
Permutational Algorithm to Simulate Survival Data
This version of the permutational algorithm generates a
dataset in which event and censoring times ...
Download / Learn more Package Citations See dependency
Download / Learn more Package Citations See dependency
Maintainer: Marie-Pierre Sylvestre (view profile)
27,806
R Packages
239,283
Dependencies
73,837
Author Associations
27,807
Publication Badges
