PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks.

ABSTRACT: Pan-genome analysis is a crucial method for studying genomic dynamics. By creating pan-genome maps for prokaryotic organisms, we can gain valuable insights into their genetic diversity and ecological adaptability. However, current analytical methods often struggle to balance accuracy and computational efficiency, and they tend to provide primarily qualitative results. This study introduces PGAP2, an integrated software package that simplifies various processes, including data quality control, pan-genome analysis, and result visualization. PGAP2 facilitates the rapid and accurate identification of orthologous and paralogous genes by employing fine-grained feature analysis within constrained regions. Our systematic evaluation with simulated and gold-standard datasets demonstrates that PGAP2

SUBMITTER: Bu C 

PROVIDER: S-EPMC12603064 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature