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Phytools specifications


Unique identifier OMICS_12499
Name Phytools
Alternative name Phylogenetic Tools for comparative biology
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.6-44
Stability Stable
methods, stats, graphics, utils, grDevices, plotrix, MASS, nlme, coda, R(≥3.2.0), combinat, rgl, msm, mnormt, maps, numDeriv, scatterplot3d, geiger, ape(≥4.0), animation, clusterGeneration, phangorn(≥2.3.1)
Maintained Yes




No version available



  • person_outline Liam J. Revell

Publication for Phylogenetic Tools for comparative biology

Phytools citations


Multiple origins of green blood in New Guinea lizards

Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] histories under the ARD model, 332 character histories under the ER model, and 282 character histories under the IR model. For all four models, we used stochastic character mapping (), implemented in phytools (), to summarize the results of multiple trait mappings onto our phylogeny using a continuous-time Markov process. The transition rate matrix estimated for each model was applied to these sim […]


Asynchronous evolution of interdependent nest characters across the avian phylogeny

Nat Commun
PMCID: 5951845
PMID: 29760391
DOI: 10.1038/s41467-018-04265-x
call_split See protocol

[…] fferent priors (Supplementary Fig. ). Thus, we only reported the results based on the equal-rate models. We generated a majority-rule consensus tree from the extracted 1000 trees using the R package, phytools with branch length estimated using a “least square” approach (Supplementary Fig. ). We mapped the states of each nest character on the consensus tree to summarize and visualize the distributi […]


Unexpectedly rapid evolution of mandibular shape in hominins

Sci Rep
PMCID: 5943523
PMID: 29743608
DOI: 10.1038/s41598-018-25309-8
call_split See protocol

[…] different rate variation models, which are compared to each other (and to a single rate, pure Brownian motion model) by means of restricted maximum likelihood fitted with the function brownieREML in phytools, in the case of a single variable, or mvBM in mvMORPH in the multivariate case. The likelihoods of individual models are contrasted to each other to find the best model by means of likelihood […]


Macroecology and macroevolution of the latitudinal diversity gradient in ants

Nat Commun
PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4
call_split See protocol

[…] hecked the marginal ancestral state probabilities from diversitree with marginal probabilities calculated from stochastic character mapping simulations using the make.simmap function in the R package phytools, and found them to be identical aside from sampling noise. We also performed a resampling procedure to evaluate whether the ancestral state pattern we recovered was sensitive to small sample […]


Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

Front Microbiol
PMCID: 5938605
PMID: 29765359
DOI: 10.3389/fmicb.2018.00803

[…] ple types using the “plot_heatmap” function in phyloseq v. 1.22.3, and visualized ordination plots using Principle Coordinate Analysis (PCoA). Finally, we used R packages vegan v. 2.4-5 (Dixon, ) and phytools v. 0.6-44 (Revell, ) to test for phylogenetic congruence between the host phylogeny and microbiome structure, using the Robinson-Foulds metric to assess topological similarity (Robinson and F […]


The response to selection in Glycoside Hydrolase Family 13 structures: A comparative quantitative genetics approach

PLoS One
PMCID: 5919626
PMID: 29698417
DOI: 10.1371/journal.pone.0196135

[…] iance matrix estimation”. shows the feasibility and accuracy of the pooled-within species co-variance estimation method. Here the Cheverud’s Random Skewer (RS) test [, ] implemented in the R package phytools [] were used to test the accuracy. A discussion of the appropriateness of the usage of this metric can be found in and references therein.Even with highly multivariate data (1024 traits), th […]


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Phytools institution(s)
University of Massachusetts Boston, MA, USA

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