The RDP-II (Ribosomal Database Project) is a database providing aligned and annotated rRNA sequences, phylogenetic trees, taxonomic hierarchies, and analysis services through its web server. It includes over 16,277 prokaryotic small subunit (SSU) rRNA sequences in Release 8.0 (June 1, 2000), with ~75% longer than 899 bp. The database also contains 2,055 eukaryotic and 1,503 mitochondrial SSU rRNA sequences. Additional unaligned sequences bring the total to over 30,000. The RDP-II provides analysis services such as rRNA probe checking, phylogenetic placement, chimeric sequence screening, automated alignment, similarity matrix production, and terminal restriction fragment polymorphism (T-RFLP) analysis. A new backbone phylogenetic tree for 217 prokaryotic SSU rRNA sequences was calculated using the WEIGHBOR algorithm. The RDP-II also offers a hierarchical set of phylogenetic trees, with a backbone tree at the top and subordinate trees below. The database is supported by two additional websites: the Biodegradative Strain Database and rrndb. The RDP-II is available at http://rdp.cme.msu.edu/ and has a mirror site in Japan. The email address for correspondence is now rdpstaff@msu.edu. Future updates include improved sequence selection tools, new phylogenetic tree creation programs, and a Version 2.0 of the T-RFLP program. The RDP-II is supported by the National Science Foundation, the US Department of Energy, and the State of Michigan. The database is used for research and provides data for recalculation of published phylogenetic trees. The RDP-II is a valuable resource for ribosomal RNA sequence analysis and phylogenetic studies.The RDP-II (Ribosomal Database Project) is a database providing aligned and annotated rRNA sequences, phylogenetic trees, taxonomic hierarchies, and analysis services through its web server. It includes over 16,277 prokaryotic small subunit (SSU) rRNA sequences in Release 8.0 (June 1, 2000), with ~75% longer than 899 bp. The database also contains 2,055 eukaryotic and 1,503 mitochondrial SSU rRNA sequences. Additional unaligned sequences bring the total to over 30,000. The RDP-II provides analysis services such as rRNA probe checking, phylogenetic placement, chimeric sequence screening, automated alignment, similarity matrix production, and terminal restriction fragment polymorphism (T-RFLP) analysis. A new backbone phylogenetic tree for 217 prokaryotic SSU rRNA sequences was calculated using the WEIGHBOR algorithm. The RDP-II also offers a hierarchical set of phylogenetic trees, with a backbone tree at the top and subordinate trees below. The database is supported by two additional websites: the Biodegradative Strain Database and rrndb. The RDP-II is available at http://rdp.cme.msu.edu/ and has a mirror site in Japan. The email address for correspondence is now rdpstaff@msu.edu. Future updates include improved sequence selection tools, new phylogenetic tree creation programs, and a Version 2.0 of the T-RFLP program. The RDP-II is supported by the National Science Foundation, the US Department of Energy, and the State of Michigan. The database is used for research and provides data for recalculation of published phylogenetic trees. The RDP-II is a valuable resource for ribosomal RNA sequence analysis and phylogenetic studies.