{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T11:27:16Z","timestamp":1772105236296,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: 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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: ARGUS is implemented in C++ and the source code is available at http:\/\/gobics.de\/software<\/jats:p>\n               <jats:p>Contact: \u00a0ibulla@uni-goettingen.de<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq159","type":"journal-article","created":{"date-parts":[[2010,4,17]],"date-time":"2010-04-17T00:13:39Z","timestamp":1271463219000},"page":"1409-1415","source":"Crossref","is-referenced-by-count":9,"title":["HIV classification using the coalescent theory"],"prefix":"10.1093","volume":"26","author":[{"given":"Ingo","family":"Bulla","sequence":"first","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]},{"given":"Anne-Kathrin","family":"Schultz","sequence":"additional","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]},{"given":"Fabian","family":"Schreiber","sequence":"additional","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]},{"given":"Ming","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]},{"given":"Thomas","family":"Leitner","sequence":"additional","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]},{"given":"Bette","family":"Korber","sequence":"additional","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"},{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]},{"given":"Burkhard","family":"Morgenstern","sequence":"additional","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]},{"given":"Mario","family":"Stanke","sequence":"additional","affiliation":[{"name":"1 Abteilung Bioinformatik, Institut f\u00fcr Mikrobiologie und Genetik, Georg-August-Universit\u00e4t G\u00f6ttingen, Goldschmidtstrasse 1, 37077 G\u00f6ttingen, Germany, 2 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 and 3 The Santa Fe Institute, Santa Fe, NM 87501, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,4,16]]},"reference":[{"key":"2023012507513181400_B1","doi-asserted-by":"crossref","first-page":"8543","DOI":"10.1128\/JVI.00463-07","article-title":"Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form","volume":"81","author":"Abecasis","year":"2007","journal-title":"J. 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