近年來生物資訊越來越受到矚目，資訊人員與生物學家合作的機會也已相當頻繁，在這兩者的相輔相成之下，對於各種生物相關的問題已發展出許多的工具，即便是同一個問題，對於不同領域的資訊人員也可能發展出不同的工具，這多少顯示出了生物資訊的難度以及競爭的激烈。

基因重組問題在生物學上相當的重要，這問題事實上早在20餘年前就有許多學者開始研究，一直到現在，每年都有新的工具被發展出來。在這篇論文中，透過不同的觀念 － 共同的基因，來偵測重組的存在，而不同於以往利用alignmemt之後，再使用sliding window的方式，來一段一段的偵測。這樣新的方式除了速度較快外，也提供了一個方法可讓使用者專注在基因片段上的重組。

由於這些工具的使用者多半依然是生物背景的研究人員，在增加工具的準確度、速度之外，方便性也是一大考量。這篇論文除了應用了新的觀點，也為使用者提供了一個相當方便的使用方式，使用者僅需從NCBI網站上，下載他們所要研究NCBI GenBank file，將這些檔案上傳到作者所提供的網站上，即可按剩餘步驟得到結果。

Concisely speaking, recombination moves chunks of sequence between genomes (ex. Fig1.a, Fig1.b, Fig1.c) and gives every allele the opportunity to determine its own destiny. Recombination is an important evolutionary process and is one of the key factors shaping the structure of genes and genomes. Moreover, it plays a major role in contributing and maintaining genetic diversity in populations. Since Recombination allows genomic regions to have different evolutionary histories, therefore no single phylogenetic tree can describe the ancestry of recombining sequences. This complicates/prevents effective use of phylogenies in tracing routes of disease transmission, determining molecular clock rates, estimating mutation bias and rate heterogeneity, and identifying sites under positive selection.

Most phylogenetic tree estimation methods assume that there is a single set of hierarchical relationships among sequences in a data set for all sites along an alignment. Mosaic sequences produced by past recombination events will violate this assumption and may lead to misleading results from a phylogenetic analysis due to the imposition of a single tree along the entire alignment. Therefore, the detection of past recombination is an important.

The fact that recombination breaks down the correlation between the evolutionary history of different regions in a genome provides the rationale used by most approaches to identify recombination in molecular sequences. One kind of the popular methods is based on the explicit reconstruction of gene trees for different parts of a sequence alignment and subsequent comparison of tree topology and branch lengths. If there are any differences between each region, these differences are used as indicators for underlying recombination events. The most widely used method of this kind is bootscanning [1].These methods for inferring recombination involve a high degree of computation since every genealogy of each region have to be inferred. Here we introduce a tool which is more convenient、more time saving and with totally different view point from others. In this method, we focus on the common genes among the viruses instead of each piece of DNA sequence. Simply speaking, gene is the blueprint of functional protein; it will affect the competition of organism for existence.

Our method is based on the principle that phylogenetic relationships derived from different genes will be similar when no recombination event has occurred. Thus, the method attempts to establish consistency in sequence relationships between different common genes. Rather than tree topologies or compatibility matrices, the method uses distance data to describe the relationships and thus avoids many of the difficulties posed by constructing and comparing tree topologies.

[1] Salminen M, Carr JK, Burke DS, and McCutchan FE: Identification of recombination breakpoints in HIV-1 by bootscanning. AIDS Res. Hum. Retroviruses 1995, 11:1423-1425.

[2] A. Michael Lindberg,1 Per Andersson, Carita Savolainen, Mick N. Mulders23 and Tapani Hovi :Evolution of the genome of Human enterovirus B : incongruence between phylogenies of the VP1 and 3CD regions indicates frequent recombination within the species. Journal of General Virology (2003), 84, 1223-1235

[3] Graham J. Etherington, Jo Dicks and Ian N. Roberts : Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination Vol. 21 no. 3 2005, pages 278-281 doi:10.1093/bioinformatics/bth500

[4] Kristoffer Forslund, Daniel H. Huson2 and Vincent Moulton : VisRD-visual recombination detection Vol. 20 no. 18 2004, pages 3654-3655 doi:10.1093/bioinformatics/bth400

[5] Korbinian Strimmer, Kristoffer Forslund, Barbara Holland, and Vincent Moulton A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Mol. Biol. Evol., 18, 1425-1434.

[6]Tran TTH, Ushijima H, Ngoc TT, Ha LD, Hayashi S, Sata T, Abe K: Recombination of genotype B and C in hepatitis B virus isolated from a Vietnamese patient with fulminant hepatitis. Jpn J Infect Dis 56:35-37, 2003.

[7]Kidd-Ljunggren, K., Miyakawa, Y. and Kidd, A. H. (2002): Genetic variability in hepatitis B virus . J. Gen. Virol., 83, 1267-1280.