Introduction The Optimal Representative Strain Selector (ORS) is a pipeline designed for the comprehensive comparative analysis of genomes, focusing on a custom set of input genomes belonging to the same bacterial species. The pipeline performs preliminary quality filtering and redundancy reduction, selecting high-quality and representative genomes for further comparison.The ORS generates three distinct scores: - Genomic Score: Based on double normalized ANI scores between selected genomes.- Ecological Score: Determined by double tracking selected genomes in a defined environment.- Functional Score: Derived from comparisons of functional gene families among selected genomes. These three scores are then merged into the final output file Representative_Score.txt. The merged score is reported in the last column named “Representative_Score”.