Building up phylogenies and inferring evolutionary relationships has always been an important task for evolutionary biologists but recently, the attention has also shifted to genome analysis related questions like pulling out genes involved in important biological functions like tumor progression. Gardini et. al. (2020) have developed a software package called Spathial for carrying out tasks, like searching genes involved in transition of one state to another. The software package has been developed in R language.
The package is based on Principal Path algorithm. The R package is available at the following website https://cran.r-project.org/web/packages/spathial/index.html. It is also available on GitHub (https://github.com/erikagardini/spathial).
Reference:
Gardini A. et. al. (2020) Spathial: an R package for the evolutionary analysis biological data. Bioinformatics 36(17):4664-4667.