title: BPhyOG: an interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes.
abstract: BACKGROUND
  Overlapping genes (OGs) in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest.
  
  
  METHODS
  BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ) and Unweighted Pair-Group Method using Arithmetic averages (UPGMA). Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint.
  
  
  CONCLUSIONS
  BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by annotations make BPhyOG a powerful web server for genomic and genetic studies. It is freely available at http://cmb.bnu.edu.cn/BPhyOG.
authors.affiliation: MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing, China. luoyq@mail.bnu.edu.cn <luoyq@mail.bnu.edu.cn>
authors.forename: Yingqin
authors.initials: Y
authors.lastname: Luo
authors.forename: Cong
authors.initials: C
authors.lastname: Fu
authors.forename: Da-Yong
authors.initials: DY
authors.lastname: Zhang
authors.forename: Kui
authors.initials: K
authors.lastname: Lin
mesh_terms: D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D005807:Genes, Overlapping; D016680:Genome, Bacterial; D020407:Internet; D016366:Open Reading Frames; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface