1. A method for identifying a horizontally transferred gene, the method comprising: defining a cuboid in a three dimensional space, wherein the cuboid encompasses fragment points corresponding to genomic fragments from a plurality of sequenced microbial genomes; dividing the cuboid into a plurality of grids; selecting one or more grids corresponding to a selected genome from the plurality of grids; classifying each of the selected grids as one of majority, minority, and mixed grids, based on number of fragment points corresponding to the selected genome in each of the selected grids; and identifying, from the minority and the mixed grids, at least one compositionally distinct genomic fragment corresponding to the horizontally transferred gene as a horizontally transferred gene fragment based on a distance ratio assessment.