A Web-Based Phylogenetic Analysis for a Query Gene

Abstract

We present a robust web server called Phytree of a query gene for phylogenetic analysis from the latest protein database with a user-friendly, interactive graphical user interface. Phytree of a query gene combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done, the corresponding sequences can be passed to the phylogenetic tree reconstruction pipelines (multiple alignment, data process, phylogenetic reconstruction, tree visualization). As the major technological innovation, selection of a meaningful subset of BLAST hits is implemented using pipeline programming and tree visualization used Java-based recursive method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required. Phytree of a query gene only needs users to copy their amino acid sequence of their query gene to the input box, and the phylogenetic tree will be built once and for all. This function is very practical for non-specialist in phylogeny. Moreover, Phytree of a query gene introduces several new methods in treatment of intermediate results, which makes it much faster, easier and more accurate, robust in phylogenetic tree reconstruction. It is specially designed for users who have no experience in phylogeny. It is freely available on our web page: http://211.69.198.144/aGene.htm.