the threshold bootstrap clustering a new approach to find families or transmission clusters within molecular quasispecies阈值引导聚类新方法找到家庭或传输集群内分子准物种.pdfVIP

The Threshold Bootstrap Clustering: A New Approach to Find Families or Transmission Clusters within Molecular Quasispecies 1,2,3. 1,4 1 1 Mattia C. F. Prosperi *, Andrea De Luca , Simona Di Giambenedetto , Laura Bracciale , 1 1 2,3. Massimiliano Fabbiani , Roberto Cauda , Marco Salemi 1 Infectious Diseases Clinic, Catholic University of the Sacred Heart, Rome, Italy, 2 Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America, 3 Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America, 4 Infectious Diseases Unit II, University Hospital of Siena, Siena, Italy Abstract Background: Phylogenetic methods produce hierarchies of molecular species, inferring knowledge about taxonomy and evolution. However, there is not yet a consensus methodology that provides a crisp partition of taxa, desirable when considering the problem of intra/inter-patient quasispecies classification or infection transmission event identification. We introduce the threshold bootstrap clustering (TBC), a new methodology for partitioning molecular sequences, that does not require a phylogenetic tree estimation. Methodology/Principal Findings: The TBC is an incremental partition algorithm, inspired by the stochastic Chinese restaurant process, and takes advantage of resampling techniques and models of sequence evolution. TBC uses as input a multiple alignment of molecular sequences and its output is a crisp partition of the taxa into an automatically determined number of clusters. By varying initi