Taxonomy and Phylogeny

  • Species2000 is an ongoing cooperative project being developed by an international team aimed at creating a database that will identify every known species in the world. The database currently includes about 40 percent of all known species.
  • LPSN - List of Prokaryotic Names With Standing in Nomenclature.
  • RDP - The ribosomal database project.
  • NCBI taxonomy browser
  • Index Fungorum - This database of fungal names contains over 370,000 names of fungi at species level and below.
  • Bacterial Nomenclature Up-to-date - a service provided by DSMZ.
  • - a database of bacterial strains, synonyms and external links.

Culture Collections

Abbreviation Culture Collection
ATCC American Type Culture Collection
CBS Fungal Biodiversity Centre, The Netherlands
CCUG Culture Collection, University of Goteborg, Sweden
CECT Colección Española de Cultivos Tipo (Spanish Type Culture Collection)
CIP Collection de l'Institute Pasteur
DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen
(German Collection of Microorganisms and Cell Cultures)
LMG The Belgian Co-ordinated Collections of Micro-organisms
UKNCC United Kingdom National Culture Collection
NRRL Northern Regional Research Center
Agricultural Research Service Culture Collection
National Center for Agricultural Utilization Research, USDA

Other helpful information about available culture collections from around the world can be found at the World Data Centre for Microorganisms.

Molecular Biology Tools and Bioinformatics

  • National Center for Biotechnology Information (NCBI)
  • ExPASy Dedicated to the analysis of protein sequences and structures.
  • EMBOSS An open source project started by the EMBnet community in order to replace proprietary systems like GCG.
  • mPUMA A software package designed to allow researchers to profile microbial communities using a de novo assembly approach to form Operational Taxonomic Units (OTUs). While originally designed to support the analysis of cpn60 based amplicons, mPUMA can be used to analyze data from any suitable DNA barcode.