Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)
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 http://www.phangorn.org.
Schliep K.P. (2011) phangorn: Phylogenetic analysis in R. Bioinformatics, 27(4) 592-593