Jill L. Wegrzyn et al. 5 Trace ﬁles FASTA ﬁles Sequence processing Sequence clustering Annotation File preparation Loading scripts TreeGenes EST module Submission ﬂat ﬁles dbEST Gene ontology Custom BLAST Figure 4: EST analysis and submission process. The EST processing and submission pipeline can support multiple projects and species (http://dendrome.ucdavis.edu/treegenes/est/). Traceﬁles are renamed, assembled, clustered, annotated, and submitted to Genbank upon the submitter’s approval. The web interface allows users to track the progress, view EST sequences, and provide basic annotation-based searches once the data has been loaded into the TreeGenes database. and one or more searchable ﬁelds. The recent increase in high-throughput sequencing projects encouraged the development of interfaces capable of dealing with the analysis of large amounts of data. In short, researchers can query thousands of sequences in a single operation. The desktop style interface assists with these searches and allows users to customize their results and organize data views. Users can perform multiple searches at one time and combine results. Data types available here currently include ESTs, EST anno- tation, traceﬁles, SNPs, primer sequences, and resequenced amplicons (including DNA extraction and tree sample information) (http://dendrome.ucdavis.edu/interface/). This interface currently accesses information for over 40 000 ESTs and nearly 8 000 resequenced amplicons. 3. AVAILABILITY, DATA SUBMISSION, FEEDBACK, AND SUPPORT The Dendrome Project and the TreeGenes database are publicly available and can be accessed at http://dendrome .ucdavis.edu/. From the website, there is access to help in the form of tutorials and a user manual. We encourage researchers to actively participate in making Dendrome and TreeGenes more accessible by submitting data and providing feedback on general usability. We are inter- ested in being able to provide a unique resource to the community, which is fully dependent on individual submissions. TreeGenes has a robust interface to submit a variety of information including sequence data and comparative mapping ﬁles through the literature database. More information on this resource can be found in http://dendrome.ucdavis.edu/TreeGenes/literature/. The dis- cussion forum available through the Dendrome Project website provides an opportunity for users to submit sug- gestions on improvements or additions to the community resources. Input relating to new functionality and additional data sources are welcome here. A help form is available for user-speciﬁc queries. This feedback form will automatically send us the inquiry, making it easier to give an accurate response. Further information is available by joining one of the TreeGenes electronic mailing lists (details on the website) or by email to info@treegenes.ucdavis.edu. 4. FUTURE DEVELOPMENT The structure of TreeGenes permits researchers to rapidly accumulate a wealth of information about a particular object or set of objects. This ﬂexible design facilitates the formulation of new hypotheses for reﬁning subsequent investigations. In addition to reﬁnement and extension of smaller scale investigations, TreeGenes can also facilitate more comprehensive approaches by allowing the investiga- tion of interactions among datasets. TreeGenes is still in a phase of rapid development. Future plans include incorpo- rating standardized gene ontology to describe phenotypic traits unique to forest trees. In addition, robust databases will be available for the submission and visualization of SNP and expression data. The advanced workspace interface will be expanded to accommodate both of these data types as well as tools to ease the analysis and comparison of this information. With an emphasis on meaningful data acquisition and interface design, TreeGenes continues to serve a critical role in the eﬃcient storage and analysis of data by the forest genetics community.