Generalized Pair Hidden Markov Model (GPHMM)
This package trains a GPHMM and computes GPHMM probabilities.
The model will is described in details in https://www.biorxiv.org/content/early/2017/12/04/228619.
install.packages('gphmm')
Note that gphmm package need compilation of C++ code.
Installing from CRAN is recommended. However, if you want to install the version from GitHub, you can do so with the following lines of code
library(devtools)
install_github("fperraudeau/gphmm")