├── README.md ├── Sample_Data ├── Input_example │ ├── Reference_genomes │ │ └── E_coli_K-12_MG1655.fasta │ └── Target_genomes │ │ ├── ASM15512v1.fna │ │ ├── ASM17195v1.fna │ │ ├── ASM2222v1.fna │ │ ├── ASM2516v1.fna │ │ ├── ASM666v1.fna │ │ ├── ASM886v1.fna │ │ ├── SRR10358485.fasta │ │ ├── SRR10358486.fasta │ │ ├── SRR10358487.fasta │ │ ├── SRR10358488.fasta │ │ ├── SRR10358489.fasta │ │ └── SRR10358491.fasta └── Output_example │ ├── E_coli_K-12_MG1655 │ └── final_output │ │ ├── E_coli_K-12_MG1655_avg_synteny_scores_100_regions.csv │ │ ├── E_coli_K-12_MG1655_avg_synteny_scores_200_regions.csv │ │ ├── E_coli_K-12_MG1655_avg_synteny_scores_40_regions.csv │ │ ├── E_coli_K-12_MG1655_avg_synteny_scores_60_regions.csv │ │ ├── E_coli_K-12_MG1655_avg_synteny_scores_80_regions.csv │ │ ├── E_coli_K-12_MG1655_avg_synteny_scores_all_regions.csv │ │ └── E_coli_K-12_MG1655_synteny_scores_per_region.csv │ └── summary_output │ ├── avg_synteny_scores_200_regions.csv │ ├── 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