2 International Journal of Plant Genomics Figure 1: Diversity of web-based resources available through the Dendrome Project and TreeGenes database. The Dendrome project (http://dendrome.ucdavis.edu/) serves as a community resource and portal to a variety of resources. These include the TreeGenes database followed by the supporting large-scale project pages, and the Dendrome Plone which is a controlled access forum. 2. CONTENT AND ORGANIZATION 2.1. Dendrome project resources The Dendrome pages are entry points to valuable links, community projects, information forums, custom tools, and the TreeGenes database (http://dendrome.ucdavis.edu/ resources/) (Figure 1). The resources available include cus- tom BLAST and FASTA services for sequence similarity searches. These services directly access all publicly available sequence data as well as custom EST or related databases. Users can submit requests for the generation and submission of a searchable database to this repository. An area for the retrieval and submission of custom scripts developed in the community of general use for the manipulation of genetic data exists. This interface allows authors to post and make available scripts and more advanced programs that they have designed including relevant documentation. The tools pages are internally curated and provide information on open source and freeware software packages that are relevant to the processing, availability, and analysis of data presented in the TreeGenes database. Links’ pages allow users to submit to and describe online resources and projects relevant to the research community. The links are submitted into one or more relevant genomic categories and are available immediately in the repository.Forms are present through the Dendrome site in order to encourage users to modify, add, and correct a variety of information. The Dendrome pages are the primary source of useful information for the research community such as upcoming events, research opportunities, and the community-curated repository of links. In addition, a discussion forum has recently been implemented to encourage users to submit questions and comments on the database as well as participate in general discussions of conifer genomics. The related Dendrome Plone (http://dendrome.ucdavis.edu/TGPlone), based on the Plone 3.0 content management platform (http://plone.org/), provides a user friendly environment for investigators to share and obtain information relating to a variety of projects. 2.2. Treegenes database overview TreeGenes (http://dendrome.ucdavis.edu/treegenes/) func- tions through a semi-automated PostgreSQL version 8.1.4- based database that consists of modules to hold a broad range of data and information for trees. This system has a front end consisting of Perl 5.8.5 scripts running in a Linux/Apache/PHP environment. The database is organized into ten diﬀerent modules that are highly connected in order to ease access and analysis of the data (Figure 2). These modules include sample tracking that holds tree source and DNA extraction information. The sequencing and primers module contains sequences from the resequencing eﬀorts as well as data describing how the sequences were generated and parameters used in their alignment and analysis. The Species module holds the taxonomy information and the Colleague Module contains information on laboratories and individu- als. There is a comparative map module that uses Cmap [2] to hold and view genetic maps, map relations, and molecular markers. The Literature module stores publications. The EST