About PEPPAN PEPPAN (Phylogeny Enhanced Pipeline for PAN-genome) is a pipeline that can construct a pan-genome from thousands of genetically diversified bacterial genomes. PEPPAN implements a combination of tree- and synteny-based approaches to identify and exclude paralogous genes, as well as similarity-based gene predictions that support consistent annotations of genes and pseudogenes in individual genomes.
Citation If you use PEPPAN please cite the pre-print in BioRxiv:
Z Zhou, M Achtman (2020) "Accurate reconstruction of the pan- and core- genomes of bacteria with PEPPA" bioRxiv, doi: https://doi.org/10.1101/2020.01.03.894154