The Ribosomal Database Project (RDP-II) is a curated database that provides ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, along with analysis services and associated computer programs. It is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing, and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu.edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities include distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees. RDP-II has been reworked to include over 9700 small subunit (SSU) rRNA sequences in aligned form and over 22,000 sequences in unaligned form. The eukaryotic alignment file has been completely reworked, resulting in a >400% increase in the number of SSU rRNA sequences. Phylogenetic trees continue to be available for the sequences in the posted SSU rRNA alignments. They have been assembled from appropriately overlapping subtrees, each of which has been inferred using maximum-likelihood analysis. Additional trees for the representative and taxonomic nodes for each aligned SSU rRNA data set are also now available. The RDP-II offers a collection of SSU and LSU rRNA secondary structure diagrams in PostScript format generated and supplied by R.Gutell and collaborators. The RDP-II World Wide Web server pages have been extensively revised. The RDP-II data and analysis services can be found at URL: http://www.cme.msu.edu/RDP. The RDP-II data can be accessed via anonymous ftp to ftp.cme.msu.edu. Currently, only the Illinois site supports an automated electronic mail server. Email correspondence with RDP-II staff should be addressed to rdp@vitro.cme.msu.edu. Those without access to Email may contact the RDP-II staff via telephone, fax, or regular mail. RDP-II plans to serve as a repository for published alignments and masks used in trees. Connections between the RDP-II and Bergey's Manual of Systematic Bacteriology will be established for data that are common to the two projects.The Ribosomal Database Project (RDP-II) is a curated database that provides ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, along with analysis services and associated computer programs. It is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing, and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu.edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities include distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees. RDP-II has been reworked to include over 9700 small subunit (SSU) rRNA sequences in aligned form and over 22,000 sequences in unaligned form. The eukaryotic alignment file has been completely reworked, resulting in a >400% increase in the number of SSU rRNA sequences. Phylogenetic trees continue to be available for the sequences in the posted SSU rRNA alignments. They have been assembled from appropriately overlapping subtrees, each of which has been inferred using maximum-likelihood analysis. Additional trees for the representative and taxonomic nodes for each aligned SSU rRNA data set are also now available. The RDP-II offers a collection of SSU and LSU rRNA secondary structure diagrams in PostScript format generated and supplied by R.Gutell and collaborators. The RDP-II World Wide Web server pages have been extensively revised. The RDP-II data and analysis services can be found at URL: http://www.cme.msu.edu/RDP. The RDP-II data can be accessed via anonymous ftp to ftp.cme.msu.edu. Currently, only the Illinois site supports an automated electronic mail server. Email correspondence with RDP-II staff should be addressed to rdp@vitro.cme.msu.edu. Those without access to Email may contact the RDP-II staff via telephone, fax, or regular mail. RDP-II plans to serve as a repository for published alignments and masks used in trees. Connections between the RDP-II and Bergey's Manual of Systematic Bacteriology will be established for data that are common to the two projects.