ProfileParsimony was an R package, built on Phangorn, to implement the Profile Parsimony approach to character weighting introduced by Faith and Trueman (2001). It also provides an implementation of Successive Approximations weighting (Farris 1969).
It incorporates modifications to phangorn that improve the speed of phylogenetic analysis, and adds support for TBR rearrangements.
It has now been integrated into the more capable package TreeSearch.
It is still possible to install the standalone package thus:
# Install the devtools package from CRAN
install.packages('devtools')
# Install the inapplicable package from github
devtools::install_github('ms609/ProfileParsimony')
# Load the package into R
library('ProfileParsimony')D. P. Faith, J. W. H. Trueman, Towards an inclusive philosophy for phylogenetic inference. Syst. Biol. 50, 331–350 (2001). doi:10.1080/10635150118627
Farris, J. S. (1969). A successive approximations approach to character weighting. Systematic Biology, 18(4), 374–385. doi:10.2307/2412182
K. P. Schliep, phangorn: phylogenetic analysis in R. Bioinformatics. 27, 592–593 (2011). doi:10.1093/bioinformatics/btq706