PanTools v3: functional annotation, classification and phylogenomics

Jonkheer, E.M.; Workum, F.J.M. van; Sheikhizadeh Anari, S.; Brankovics, B.; Haan, J.R. de; Berke, Lidija; Lee, T.A.J. van der; Ridder, D. de; Smit, S.


The ever-increasing number of sequenced genomes necessitates the development of pangenomic approaches for comparative genomics. Introduced in 2016, PanTools is a platform that allows pangenome construction, homology grouping and pangenomic read mapping. The use of graph database technology makes PanTools versatile, applicable from small viral genomes like SARS-CoV-2 up to large plant or animal genomes like tomato or human. Here, we present our third major update to PanTools that enables the integration of functional annotations and provides both gene-level analyses and phylogenetics.