Installation

PHONEMeS-ILP

For the installation of the most recent ILP implementation of PHONEMeS the user can do this directly from GitHub by using the devtools package:

# Install PHONEMeS from Github using devtools
install.packages('devtools') # in case devtools hasn't been installed
library(devtools)
install_github('saezlab/PHONEMeS-ILP')

Otherwise users can install PHONEMeS directly from the source after downloading the source (tar file) and typing in R command line the following:

# or download the source file from GitHub and install from source
install.packages('path_to_extracted_PHONEMeS_directory', repos = NULL, type="source")

For PHONEMeS-ILP depedencies, please read carefully the documentation of the PHONEMeS-ILP package.

PHONEMeS-stoch

For the installation of the old stochastic implementation (PHONEMeS-stoch), download the tar-file of the package (can be found here). Open R and type:

install.packages("PHONEMeS_0.2.7.tar.gz", repos=NULL)