BacMet: antibacterial biocide and metal resistance genes database. - Chandan Pal; Johan Bengtsson-Palme; Christopher Rensing; Erik Kristiansson; D. G. Joakim Larsson (Nucleic Acids Res., 2014)

FARAO: the flexible all-round annotation organizer. - Rickard Hammarén; Chandan Pal; Johan Bengtsson-Palme (Bioinform., 2016)

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2. - Johan Bengtsson-Palme; Kaisa Thorell; Christian Wurzbacher; Åsa Sjöling; R. Henrik Nilsson (Ecol. Informatics, 2016)

Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker. - Johan Bengtsson-Palme; Rodney T. Richardson; Marco Meola; Christian Wurzbacher; Émilie D. Tremblay; Kaisa Thorell; Kärt Kanger; K. Martin Eriksson; Guillaume J. Bilodeau; Reed M. Johnson; Martin Hartmann; R. Henrik Nilsson (Bioinform., 2018)

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. - R. Henrik Nilsson; Karl-Henrik Larsson; Andy F. S. Taylor; Johan Bengtsson-Palme; Thomas S. Jeppesen; Dmitry Schigel; Peter Kennedy; Kathryn Picard; Frank Oliver Glöckner; Leho Tedersoo; Irja Saar; Urmas Kõljalg; et al. (Nucleic Acids Res., 2019)

CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data. - Anna Abramova; Adriana Osinska; Haveela Kunche; Emil Burman; Johan Bengtsson-Palme (Bioinform., 2021)