I trying to perform a comparative genome analysis by BPGA, between two Streptomyces strains.
The pipeline very correctly takes the two Protein FASTA files (downloaded from NCBI), as input.
My query is that the core/accessory/uniques genes should get colored differently as we see in the manual, but it's not the case with my results. Even though the core and unique genes are identified, both the bars are colored with the same color. Why is it so?
Did the parameters I chose created this problem? Or such results are expected?