CRAN Task View: Phylogenetics

Maintainer:William Gearty, Brian O'Meara, Jacob Berv, Gustavo A. Ballen, Diniz Ferreira, Hilmar Lapp, Lars Schmitz, Martin R. Smith, Nathan S. Upham, Jonathan A. Nations
Contact:willgearty at gmail.com
Version:2022-10-25
URL:https://CRAN.R-project.org/view=Phylogenetics
Source:https://github.com/cran-task-views/Phylogenetics/
Contributions:Suggestions and improvements for this task view are very welcome and can be made through issues or pull requests on GitHub or via e-mail to the maintainer address. For further details see the Contributing guide.
Citation:William Gearty, Brian O'Meara, Jacob Berv, Gustavo A. Ballen, Diniz Ferreira, Hilmar Lapp, Lars Schmitz, Martin R. Smith, Nathan S. Upham, Jonathan A. Nations (2022). CRAN Task View: Phylogenetics. Version 2022-10-25. URL https://CRAN.R-project.org/view=Phylogenetics.
Installation:The packages from this task view can be installed automatically using the ctv package. For example, ctv::install.views("Phylogenetics", coreOnly = TRUE) installs all the core packages or ctv::update.views("Phylogenetics") installs all packages that are not yet installed and up-to-date. See the CRAN Task View Initiative for more details.

Overview

The history of life unfolds within a phylogenetic context, and phylogenetic trees (often shortened to “trees”) are developed to represent this evolutionary history. Comparative phylogenetic methods are statistical approaches for analyzing historical patterns along such phylogenetic trees. This task view describes R packages that (i) facilitate the handling, manipulation and analysis of phylogenetic trees; (ii) implement comparative phylogenetic methods; (iii) apply phylogenetic methods to specific disciplines. This is an active research area and much of the information is subject to change. Many important packages are not on CRAN: either they were formerly on CRAN and were later archived (for example, if they failed to incorporate necessary changes as R is updated) or they are developed elsewhere and are not yet available on CRAN. Such packages may be found on GitHub, R-Forge, Bioconductor, or authors’ websites. At least ten packages start as phy* in this domain, including two pairs of similarly named packages (phytools and phylotools, phylobase and phybase); users are encouraged to read and distinguish carefully between package names.

If you have any questions, feel free to reach out to the task view maintainers or the maintainers of specific packages. Questions may also be directed to the R-SIG-Phylo mailing-list after subscription.

Scope

Core packages

Tasks

Packages within the task view fall within one or more of the following task categories:

  1. Working with trees in R: packages dedicated to the handling, manipulation, and visualization of phylogenetic data
  2. Building trees in R: packages for phylogenetic inference and tree simulation
  3. Comparative phylogenetic methods: packages for performing various comparative phylogenetic methods, including those dealing with trait evolution and diversification
  4. Phylogenetics in other fields: packages designed to perform field-specific phylogenetic analyses, including paleontology, community ecology, biogeography, and genetics
  5. Other useful packages and miscellany: packages that are useful for performing phylogenetic analyses, such as taxonomic matching

Working with trees in R

Getting trees into R

Tree manipulation

Tree visualization

Tree comparison

Tree building in R

Phylogenetic inference

Divergence times

Tree simulations

Phylogenetic comparative methods

Ancestral state reconstruction

Trait evolution

Trait simulations

Diversification analysis

Phylogenetics in specific fields

Morphometrics

Time series and paleontology

Community and microbial ecology

Phyloclimatic modeling

Phylogeography and biogeography

Epidemiology

See the Epidemiology task view for details about packages useful for epidemiology, including phylogenetic epidemiology.

Omics

Gene tree–species tree and species delimitation

Other useful packages and miscellany

Taxonomy

Interactions with other programs

References

CRAN packages

Core:ape, geiger, phylobase, phytools.
Regular:adephylo, adiv, apex, aphid, aphylo, apTreeshape, BAMMtools, beastier, beautier, betapart, BoSSA, brms, brranching, CALANGO, caper, castor, Claddis, convevol, DAMOCLES, DDD, deeptime, dendextend, dispRity, distory, diversitree, entropart, epm, evobiR, EvoPhylo, FossilSim, geomorph, ggmuller, ggplot2, GUniFrac, hisse, HMPTrees, idendr0, ips, markophylo, MCMCglmm, metacoder, metafor, motmot, MPSEM, mvMORPH, ouch, OUwie, paleobuddy, paleotree, paleoTS, PBD, PCPS, perfectphyloR, phangorn, phyclust, phyext2, phylocanvas, phyloclim, PHYLOGR, phylogram, phylolm, phyloregion, phylosignal, phylotate, phylotools, phyloTop, phyreg, picante, pmc, Quartet, Revticulate, rncl, RNeXML, Rogue, rotl, RPANDA, Rphylopars, RRPP, secsse, SigTree, strap, surface, SYNCSA, taxize, TBRDist, TESS, tidytree, tracerer, treebase, treedater, TreeDist, treeducken, TreeSearch, TreeSim, treespace, TreeTools, vegan, windex.

Other resources