The association studies in bacterial genomes have always been an area of interest for microbial geneticists. Recently, Sexton C.E. et. al.(2018) have developed an R package for carrying out association studies amongst orthologous genes in bacterial genomes. The package is called MAGNAMWAR which stands for Mono- Associated GNotobiotic Animals Metagenome Wide association studies in R.
MAGNAMWAR is available freely on CRAN website
Sexton C.E. et. al.(2018) MAGNAMWAR: An R package for genome wide association studies of bacterial orthologs. Bioinformatics 34(11) 1951-1952.