phangorn: phangorn-package – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

phangorn-package

Phylogenetic analysis in R

Description

Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)

Details

The complete list of functions can be displayed with library(help = phangorn).

Further information is available in several vignettes. To show the available vignettes in an HTML browser type browseVignettes("phangorn").

`Trees`	Constructing phylogenetic trees (source, pdf)
`phangorn-specials`	Advanced features (source, pdf)
`Ancestral`	Ancestral sequence reconstruction (source, pdf)
`Networx`	Splits and Networx (source, html)

The first vignette (to display type vignette('Trees')) gives an introduction in phylogenetic analysis with phangorn. The second vignette (phangorn-special) covers more advanced feature like defining special character spaces and things which fit nowhere else. More information on phangorn can be found on https://www.phangorn.org/.

Author(s)

Klaus Schliep

Maintainer: Klaus Schliep <klaus.schliep@gmail.com>

References

Schliep K.P. (2011) phangorn: Phylogenetic analysis in R. Bioinformatics, 27(4) 592-593

phangorn

Phylogenetic Reconstruction and Analysis

v2.7.0

GPL (>= 2)

Authors

Klaus Schliep [aut, cre] (<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis [aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de Oliveira Martins [aut] (<https://orcid.org/0000-0001-5247-1320>), Alastair Potts [aut], Tim W. White [aut], Cyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi [ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam Revell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb], Brian O'Meara [ctb], Long Qu [ctb]

Initial release