Curated ecoli datasets for prokaryotic pangenomics

<br>Curated <i>E. coli</i> GFF dataset – A quality-controlled set of genome assemblies in GFF3 format, standardized for direct PGAP2 input. These files have consistent annotation structure to support accurate gene clustering and pan-genome construction.<code>gold_EC_all.csv</code> – A comprehensive clustering result that includes both orthologous and paralogous genes.<code>gold_EC_unpara.csv</code> – A refined clustering result containing only orthologous genes (paralogues excluded).Other intermediate steps and scripts are available at: https://github.com/bucongfan/PGAP2_benchmark.<br>For using the latest version of our software or for any inquiries, please visit: https://github.com/bucongfan/PGAP2