title: Easy-to-use phylogenetic analysis system for hepatitis B virus infection.
abstract: OBJECTIVE
  The molecular phylogenetic analysis has been broadly applied to clinical and virological study. However, the appropriate settings and application of calculation parameters are difficult for non-specialists of molecular genetics. In the present study, the phylogenetic analysis tool was developed for the easy determination of genotypes and transmission route.
  
  
  METHODS
  A total of 23 patients of 10 families infected with hepatitis B virus (HBV) were enrolled and expected to undergo intrafamilial transmission. The extracted HBV DNA were amplified and sequenced in a region of the S gene.
  
  
  RESULTS
  The software to automatically classify query sequence was constructed and installed on the Hepatitis Virus Database (HVDB). Reference sequences were retrieved from HVDB, which contained major genotypes from A to H. Multiple-alignments using CLUSTAL W were performed before the genetic distance matrix was calculated with the six-parameter method. The phylogenetic tree was output by the neighbor-joining method. User interface using WWW-browser was also developed for intuitive control. This system was named as the easy-to-use phylogenetic analysis system (E-PAS). Twenty-three sera of 10 families were analyzed to evaluate E-PAS. The queries obtained from nine families were genotype C and were located in one cluster per family. However, one patient of a family was classified into the cluster different from her family, suggesting that E-PAS detected the sample distinct from that of her family on the transmission route.
  
  
  CONCLUSIONS
  The E-PAS to output phylogenetic tree was developed since requisite material was sequence data only. E-PAS could expand to determine HBV genotypes as well as transmission routes.
authors: The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa             Department of Biochemistry and Cell Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya             Department of Pediatrics, Eastern Yokohama Hospital, Yokohama             SRL, Inc. Tokyo, Japan.
authors: Masaya
authors: M
authors: Sugiyama
authors: Ayano
authors: A
authors: Inui
authors: Tadasu
authors: T
authors: Shin-I
authors: Haruki
authors: H
authors: Komatsu
authors: Motokazu
authors: M
authors: Mukaide
authors: Naohiko
authors: N
authors: Masaki
authors: Kazumoto
authors: K
authors: Murata
authors: Kiyoaki
authors: K
authors: Ito
authors: Makoto
authors: M
authors: Nakanishi
authors: Tomoo
authors: T
authors: Fujisawa
authors: Masashi
authors: M
authors: Mizokami