Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications

• DOI: 10.1093/bioinformatics/btae526
• Publication Date: 2024-08-24T21:14:05Z
• Authors: Steven B Cannon; Hyun-Oh Lee; Nathan T Weeks; Joel Berendzen
• Keywords: Evolution, Molecular; 0301 basic medicine; 03 medical and health sciences; Gene Duplication; Multigene Family; Molecular Sequence Annotation; Genomics; Software

Identification of allelic or corresponding genes (pan-genes) within a species genus is important for discovery biologically significant genetic conservation and variation. Similarly, identification orthologs (gene families) across wider evolutionary distances understanding the basis similar differing traits. Especially in plants, several complications make pan-genes gene families challenging, including whole-genome duplications, rate differences among lineages, varying qualities assemblies annotations. Here, we document distribute set workflows that have used to address these problems.