PanTools v3: functional annotation, classification and phylogenomics
Eef M. Jonkheer, Dirk‐Jan M. van Workum, Siavash Sheikhizadeh Anari, Balázs Brankovics, Jorn R. de Haan, Lidija Berke, Théo van der Lee, Dick de Ridder, Sandra Smit
Abstract
SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: PanTools is implemented in Java 8 and released under the GNU GPLv3 license. Software and documentation are available at https://git.wur.nl/bioinformatics/pantools. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.