Phytozome is a comparative platform for green plant genomics that provides a centralized hub for plant genome and gene family data and analysis. It allows users to explore the evolutionary history of plant genes at the sequence, gene structure, gene family, and genome organization levels. Phytozome includes data from 25 complete plant genomes, including all land plants and selected algae sequenced at the Joint Genome Institute (JGI), as well as selected species sequenced elsewhere. The platform offers a comprehensive plant genome database and web portal, providing powerful comparative genomics tools to link model systems with other economically and ecologically important plants. Phytozome integrates a variety of open-source components and custom visualization tools for gene family search, inspection, and evaluation. It includes tools for text and sequence search, gene family and gene page views, and genome-centric views. The platform supports gene family construction using distance-based methods, which are generally fast and scalable but rely on a single score to characterize evolutionary divergence. Distance-plus-character-based methods use distance scores and a simple threshold to build initial gene proto-families, followed by phylogenetic tree construction based on discriminatory residues. Phytozome provides access to a wide range of genomic data, including genome assemblies, gene structure GFF3 files, transcript, coding, and peptide sequences, as well as functional annotations. Users can search for genes and gene families using keyword or sequence similarity searches, and the platform offers tools for retrieving and analyzing gene families. Phytozome also includes a BioMart data query tool for gene families and genome annotations, and allows users to customize the display options for gene pages. Phytozome is continuously updated with new genomes and features, and is expected to include genomic variation data and expression data in future releases. The platform is available for download by the end of 2011, and is licensed for distribution to end users. Phytozome is a valuable resource for the plant science research community, providing a platform for genome-informed investigations of plant evolution and transferring functional information from model plants to economically or ecologically important plants.Phytozome is a comparative platform for green plant genomics that provides a centralized hub for plant genome and gene family data and analysis. It allows users to explore the evolutionary history of plant genes at the sequence, gene structure, gene family, and genome organization levels. Phytozome includes data from 25 complete plant genomes, including all land plants and selected algae sequenced at the Joint Genome Institute (JGI), as well as selected species sequenced elsewhere. The platform offers a comprehensive plant genome database and web portal, providing powerful comparative genomics tools to link model systems with other economically and ecologically important plants. Phytozome integrates a variety of open-source components and custom visualization tools for gene family search, inspection, and evaluation. It includes tools for text and sequence search, gene family and gene page views, and genome-centric views. The platform supports gene family construction using distance-based methods, which are generally fast and scalable but rely on a single score to characterize evolutionary divergence. Distance-plus-character-based methods use distance scores and a simple threshold to build initial gene proto-families, followed by phylogenetic tree construction based on discriminatory residues. Phytozome provides access to a wide range of genomic data, including genome assemblies, gene structure GFF3 files, transcript, coding, and peptide sequences, as well as functional annotations. Users can search for genes and gene families using keyword or sequence similarity searches, and the platform offers tools for retrieving and analyzing gene families. Phytozome also includes a BioMart data query tool for gene families and genome annotations, and allows users to customize the display options for gene pages. Phytozome is continuously updated with new genomes and features, and is expected to include genomic variation data and expression data in future releases. The platform is available for download by the end of 2011, and is licensed for distribution to end users. Phytozome is a valuable resource for the plant science research community, providing a platform for genome-informed investigations of plant evolution and transferring functional information from model plants to economically or ecologically important plants.