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Background  The availability of 12 fully sequenced  Drosophila  species genomes provides an excellent opportunity to explore the evolutionary mechanism, structure and function of gene families in  Drosophila . Currently, several important resources, such as FlyBase, FlyMine and DroSpeGe, have been devoted to integrating genetic, genomic, and functional data of  Drosophila  into a well-organized form. However, all of these resources are gene-centric and lack the information of the gene families in  Drosophila .    Description  FlyPhy is a comprehensive phylogenomic analysis platform devoted to analyzing the genes and gene families in  Drosophila . Genes were classified into families using a graph-based Markov Clustering algorithm and extensively annotated by a number of bioinformatic tools, such as basic sequence features, functional category, gene ontology terms, domain organization and sequence homolog to other databases. FlyPhy provides a simple and user-friendly web interface to allow users to browse and retrieve the information at multiple levels. An outstanding feature of the FlyPhy is that all the retrieved results can be added to a workset for further data manipulation. For the data stored in the workset, multiple sequence alignment, phylogenetic tree construction and visualization can be easily performed to investigate the sequence variation of each given family and to explore its evolutionary mechanism.    Conclusion  With the above functionalities, FlyPhy will be a useful resource and convenient platform for the  Drosophila  research community. The FlyPhy is available at   .

FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families