Title
HIV classification using the coalescent theory.
Abstract
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.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.ARGUS is implemented in C++ and the source code is available at http://gobics.de/software.
Year
DOI
Venue
2010
10.1093/bioinformatics/btq159
Bioinformatics
Keywords
Field
DocType
recombinant form,hiv classification,classification hypothesis,coalescent theory,coalescent model,hiv sequence,hiv recombinants,correct classification,ancestral recombination graph,plausible alternative classification,program argus,scores classification,classification system,monte carlo method,satisfiability
Coalescent theory,Phylogenetic tree,Markov chain Monte Carlo,Source code,Computer science,Word error rate,Markov chain,Argus,Bioinformatics,CRFS
Journal
Volume
Issue
ISSN
26
11
1367-4811
Citations 
PageRank 
References 
1
0.36
8
Authors
8
Name
Order
Citations
PageRank
Ingo Bulla1525.15
Anne-Kathrin Schultz2714.36
Fabian Schreiber3916.01
Ming Zhang48918.62
Thomas Leitner5492.53
Bette Korber6858.20
B Morgenstern7109790.87
M Stanke853051.45