The Ribosomal Database Project (RDP-II) has introduced new features to enhance rRNA sequence analysis for microbial ecology. Key updates include quality control for all rRNA sequences, including chimera detection, and the introduction of myRDP Space, a web tool allowing researchers to upload and manage their own sequence data in alignment with the RDP's public data. New video tutorials and detailed information about RDP data and functions are available on the RDP-II website. As of September 2006, the RDP maintained 262,030 aligned and annotated rRNA sequences, with 84,442 from cultivated bacteria and 177,588 from environmental samples. These sequences are used to link taxonomy and phylogeny. The RDP updates its data monthly from INSDC, aligning new sequences using RNACAD, a grammar-based aligner. All sequences are tested for anomalies using Pintail, with at least 5% of rRNA records flagged as anomalous. myRDP Space allows users to maintain private sequence collections, which are aligned with the RDP's public alignment. Researchers can share data with others and access tools for sequence analysis. The myRDP Pipeline processes environmental sequences, providing quality-controlled, aligned sequences for analysis. It includes tools for sequence trimming, quality control, and alignment. New analysis services include the Hierarchy Browser, Publication View, Sequence Carts, Sequence Match, RDP Classifier, Library Compare, and Tree Tool. These tools enhance the ability to compare microbial communities, analyze sequence data, and visualize phylogenetic relationships. Download formats include FASTA, PHYLIP, and distance matrices for various phylogenetic analyses. The RDP-II website provides access to these tools and services, along with support contact information. The project is supported by various funding sources and acknowledges contributions from numerous researchers. The RDP-II aims to provide reliable, high-throughput rRNA sequence analysis for microbial ecology and related fields.The Ribosomal Database Project (RDP-II) has introduced new features to enhance rRNA sequence analysis for microbial ecology. Key updates include quality control for all rRNA sequences, including chimera detection, and the introduction of myRDP Space, a web tool allowing researchers to upload and manage their own sequence data in alignment with the RDP's public data. New video tutorials and detailed information about RDP data and functions are available on the RDP-II website. As of September 2006, the RDP maintained 262,030 aligned and annotated rRNA sequences, with 84,442 from cultivated bacteria and 177,588 from environmental samples. These sequences are used to link taxonomy and phylogeny. The RDP updates its data monthly from INSDC, aligning new sequences using RNACAD, a grammar-based aligner. All sequences are tested for anomalies using Pintail, with at least 5% of rRNA records flagged as anomalous. myRDP Space allows users to maintain private sequence collections, which are aligned with the RDP's public alignment. Researchers can share data with others and access tools for sequence analysis. The myRDP Pipeline processes environmental sequences, providing quality-controlled, aligned sequences for analysis. It includes tools for sequence trimming, quality control, and alignment. New analysis services include the Hierarchy Browser, Publication View, Sequence Carts, Sequence Match, RDP Classifier, Library Compare, and Tree Tool. These tools enhance the ability to compare microbial communities, analyze sequence data, and visualize phylogenetic relationships. Download formats include FASTA, PHYLIP, and distance matrices for various phylogenetic analyses. The RDP-II website provides access to these tools and services, along with support contact information. The project is supported by various funding sources and acknowledges contributions from numerous researchers. The RDP-II aims to provide reliable, high-throughput rRNA sequence analysis for microbial ecology and related fields.