Fruit flies have been studied for many years, and one species of them in particular, D. melanogaster, has been heavily used in genetic research and is a very important model organism for understanding genetic, developmental, cellular, ecological, and evolutionary processes. With rapid development of molecular biology and genetics, better understanding of the genomes of Drosophila species will be a great help for other research activities on fruit fly, so come the Berkeley Drosophila Genome Project (www.fruitfly.org) and FlyBase (flybase.org). With ever-developing large-scale sequencing technologies, twelve fly genomes are available and accessible online now. And this has paved the way for genomic comparisons between drosophila genomes, which serve as a significant base for functional genomics and provide an important advance for understanding sequence-structure-function relationships of fly genes between Drosophila species and for studying evolutionary changes among the species. Many progresses have been made in comparative genomics for Drosophila species in recent years. Scientists found that Drosophila species are quite diverse and tremendously differ from each other among species, genetically speaking, more than a platypus differs from a primate according to genome comparisons of the fruit fly species.

For facilitating the progress of comparative genomics in Drosophila, the research and development of effective and powerful phylogenomic tools and analysis platforms is critical works which will provide a convenient aid to Drosophila biologists. The most familiar two web resources of fruit fly for Drosophila researchers may be Berkeley Drosophila Genome Project (BDGP) and FlyBase where much information of Drosophila genes and genomes are available and a number of analysis tools are also integrated for analyzing the data thereof. Other web sites such as AAA and FlyMine are also useful resources for Drosophila biologists. However, all of these resources lack the content of the protein family data for Drosophila species, and there was no comprehensive database focusing on fly protein families reported elsewhere. So we analyzed the protein-coding sequences of 12 fruit fly genomes with TribeMCL software, and then constructed a comprehensive database of putative protein families with related annotation information of fruit fly species. And then a web platform was designed for users to retrieve the data in our database for further relevant phylogenomics analysis, where a lot of bioinformatics tools including sequence similarity comparison tools, multi-sequence alignment programs and phylogeny softwares were incorporated. Users can easily get the protein families information of their interest as well as other relevant detail annotations of genes through the user-friendly web interface and analyze the data efficiently and conveniently using the tools thereof.