title: FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.
abstract: 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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  With the above functionalities, FlyPhy will be a useful resource and convenient platform for the Drosophila research community. The FlyPhy is available at http://bioinformatics.zj.cn/fly/ .
authors.affiliation: Institute of Biomedical Informatics/Zhejiang Provincial Key Laboratory of Medical Genetics, Wenzhou Medical College, Wenzhou, PR China. iamwujy@yahoo.com.cn
authors.forename: Jinyu
authors.initials: J
authors.lastname: Wu
authors.forename: Xiang
authors.initials: X
authors.lastname: Xu
authors.forename: Jian
authors.initials: J
authors.lastname: Xiao
authors.forename: Long
authors.initials: L
authors.lastname: Xu
authors.forename: Huiguang
authors.initials: H
authors.lastname: Yi
authors.forename: Shengjie
authors.initials: S
authors.lastname: Gao
authors.forename: Jing
authors.initials: J
authors.lastname: Liu
authors.forename: Qiyu
authors.initials: Q
authors.lastname: Bao
authors.forename: Fangqing
authors.initials: F
authors.lastname: Zhao
authors.forename: Xiaokun
authors.initials: X
authors.lastname: Li
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D004330:Drosophila / Q000235:genetics*; D017344:Genes, Insect; D049750:Genome, Insect / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D010802:Phylogeny; D012984:Software; D014584:User-Computer Interface