phytools

swMATH10003CRANphytoolsMaRDI QIDQ21979

Phylogenetic Tools for Comparative Biology (and Other Things)

Liam J. Revell

Last update: 9 January 2024

Copyright license: GNU General Public License, version 3.0, GNU General Public License, version 2.0

Software version identifier: 1.5-1, 0.0-8, 0.1-0, 0.1-2, 0.1-5, 0.1-6, 0.1-7, 0.1-8, 0.1-9, 0.2-0, 0.2-1, 0.2-20, 0.2-30, 0.2-40, 0.2-50, 0.2-70, 0.2-80, 0.2-90, 0.3-10, 0.3-72.1, 0.3-72, 0.3-93, 0.4-05, 0.4-21, 0.4-31, 0.4-45, 0.4-56, 0.4-60, 0.5-00, 0.5-10, 0.5-20, 0.5-38, 0.5-64, 0.6-00, 0.6-20, 0.6-44, 0.6-60, 0.6-99, 0.7-20, 0.7-47, 0.7-70, 0.7-80, 0.7-90, 1.0-1, 1.0-3, 1.2-0, 1.9-16, 2.0-3, 2.1-1

Source code repository: https://github.com/cran/phytools

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.

Related Items (52)

Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements ⋮ A comparison of ancestral state reconstruction methods for quantitative characters ⋮ On the estimation of nested Archimedean copulas: a theoretical and an experimental comparison ⋮ ontophylo ⋮ TML ⋮ Identical inferences about correlated evolution arise from ancestral state reconstruction and independent contrasts ⋮ The shape of phylogenies under phase-type distributed times to speciation and extinction ⋮ Comparing the rankings obtained from two biodiversity indices: the fair proportion index and the Shapley value ⋮ Bioinformatics. Volume I. Data, sequence analysis, and evolution ⋮ geiger ⋮ convevol ⋮ GIFT ⋮ DDD ⋮ funspace ⋮ windex ⋮ deeptime ⋮ paleotree ⋮ hisse ⋮ pirouette ⋮ RevGadgets ⋮ Fast likelihood calculation for multivariate Gaussian phylogenetic models with shifts ⋮ pmc ⋮ Functional and Phylogenetic Ecology in R ⋮ BAT ⋮ adiv ⋮ Rtapas ⋮ pez ⋮ RRphylo ⋮ arakno ⋮ Claddis ⋮ OUwie ⋮ Working out the bipedal walking expenditure of energy based on foot morphology of different hominid genera: implications for foot evolution ⋮ FishPhyloMaker ⋮ perfectphyloR ⋮ MonoPhy ⋮ tapnet ⋮ recluster ⋮ bite ⋮ learnPopGen ⋮ treestartr ⋮ PBD ⋮ evobiR ⋮ datelife ⋮ Assessing phenotypic correlation through the multivariate phylogenetic latent liability model ⋮ Modeling rate of adaptive trait evolution using Cox-Ingersoll-Ross process: an approximate Bayesian computation approach ⋮ corHMM ⋮ mvMORPH ⋮ sensiPhy ⋮ PhySortR ⋮ treespace ⋮ RPANDA ⋮ Rphylopars

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