Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index.

ABSTRACT: Classification of viral sequences should be fast, objective, accurate and reproducible. Most methods that classify sequences use either pair-wise distances or phylogenetic relations, but cannot discern when a sequence is unclassifiable. The branching index (BI) combines distance and phylogeny methods to compute a ratio that quantifies how closely a query sequence clusters with a subtype clade. In the hypothesis-testing framework of statistical inference, the BI is compared with a threshold to test whether sufficient evidence exists for the query sequence to be classified among known sequences. If above the threshold, the null hypothesis of no support for the subtype relation is rejected and the sequence is taken as belonging to the subtype clade with which it clusters on the tree. This stu

SUBMITTER: Hraber P 

PROVIDER: S-EPMC2754793 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature