title: HIV classification using the coalescent theory.
abstract: BACKGROUND
  Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns.
  
  
  RESULTS
  We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. It reconstructs ancestral recombination graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov chain Monte Carlo approach. ARGUS was able to distinguish the correct classification with a low error rate from plausible alternative classifications in simulation studies with realistic parameters. We applied our algorithm to decide between two recently debated alternatives in the classification of CRF02 of HIV-1 and find that CRF02 is indeed a recombinant of Subtypes A and G.
  
  
  BACKGROUND
  ARGUS is implemented in C++ and the source code is available at http://gobics.de/software.
authors.affiliation: Abteilung Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany. ibulla@uni-goettingen.de
authors.forename: Ingo
authors.initials: I
authors.lastname: Bulla
authors.forename: Anne-Kathrin
authors.initials: AK
authors.lastname: Schultz
authors.forename: Fabian
authors.initials: F
authors.lastname: Schreiber
authors.forename: Ming
authors.initials: M
authors.lastname: Zhang
authors.forename: Thomas
authors.initials: T
authors.lastname: Leitner
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
authors.forename: Burkhard
authors.initials: B
authors.lastname: Morgenstern
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
mesh_terms: D000465:Algorithms; D006678:HIV / Q000145:classification* / Q000235:genetics; D015497:HIV-1 / Q000145:classification; D008390:Markov Chains; D010802:Phylogeny; D017422:Sequence Analysis, DNA
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