SlidingBayes: Exploring recombination using a sliding window approach based on Bayesian phylogenetic inference

Bioinformatics

Volumn 21, Issue 7, 2005, Pages 1274-1275

  Paraskevis, D ^a,b   Deforche, K ^a   Lemey, P ^a   Magiorkinis, G ^b   Hatzakis, A ^b   Vandamme, A M ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b UNIVERSITY OF ATHENS MEDICAL SCHOOL   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NUCLEOTIDE; PROTEINASE; RNA DIRECTED DNA POLYMERASE;

AMINO ACID SEQUENCE; ARTICLE; BAYES THEOREM; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC RECOMBINATION; HUMAN IMMUNODEFICIENCY VIRUS 1; MAXIMUM LIKELIHOOD METHOD; MOLECULAR PHYLOGENY; MONTE CARLO METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROBABILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TAXONOMY; VIRUS RECOMBINANT;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 16344380414     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti139     Document Type: Article

References (18)

1. Abecasis,A., Paraskevis,D., Epalanga,M., Fonseca,M., Burity,F., Bartolomeu,J., Carvalho,A.P., Gomes,P., Vandamme,A.-M. and Camacho,R. (2005) HIV-1 genetic variants circulation in the North of Angola. Infec. Gene. and Evol., in press.
2. Bailes,E., Gao,F., Bibollet-Ruche,F., Courgnaud,V., Peeters,M., Marx,P.A., Hahn,B.H. and Sharp,P.M. (2003) Hybrid origin of SIV in chimpanzees. Science, 13, 1713.
3. Bollyky,P.L., Rambaut,A., Harvey,P.H. and Holmes,E.C. (1996) Recombination between sequences of hepatitis B virus from different genotypes. J. Mol. Evol., 42, 97-102.
4. Courgnaud,V., Formenty,P., Akoua-Koffi,C., Noe,R., Boesch,C., Delaporte,E. and Peeters,M. (2003) Partial molecular characterization of two simian immunodeficiency viruses (SIV) from African colobids: SIV wrc from Western red colobus (Piliocolobus badius) and SIVolc from olive colobus (Procolobus verus). J. Virol., 77, 744-748.
5. Felsenstein,J. (1984) Distance methods for inferring phylogenies: a Justification. Evolution, 38, 16-24.
6. Holmes,E.C., Worobey,M. and Rambaut,A. (1999) Phylogenetic evidence for recombination in dengue virus. Mol. Biol. Evol., 16 405-409.
7. Huelsenbeck,J.P., Ronquist,F., Nielsen,R. and Bollback,J.P. (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science, 294, 2310-2314.
8. Huelsenbeck,J.P., Larget,B., Miller,R.E. and Ronquist,F. (2002) Potential applications and pitfalls of bayesian inference of phylogeny. Syst. Biol., 51, 673-688.
9. Korber,B., Muldoon,M., Theiler,J., Gao,F., Gupta,R., Lapedes,A., Hahn,B.H., Wolinsky,S. and Bhattacharya,T. (2000) Timing the ancestor of the HIV-1 pandemic strains. Science, 288, 1789-1796.
10. Lole,K.S., Bollinger,R.C., Paranjape,R.S., Gadkari,D., Kulkarni,S.S., Novak,N.G., Ingersoll,R., Sheppard,H.W. and Ray,S.C. (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol., 73, 152-160.
11. Paraskevis,D., Lemey,P., Salemi,M., Suchard,M., Van de Peer,Y. and Vandamme,A.M. (2003) Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using Bayesian inference: implications for the origin of HIV-1. Mol. Biol. Evol., 20, 1986-1996.
12. Paraskevis,D., Deforche,K., Abecasis,A., Camacho,R. and Vandamme,A.-M. (2005) Analysis of complex HIV-1 intersubtype recombinants using a Bayesian scanning method. Infec. Gene. and Evol., in press.
13. Robertson,D.L., Hahn,B.H. and Sharp,P.M. (1995a) Recombination in AIDS Viruses. J. Mol. Evol., 40, 249-259.
14. Robertson,D.L., Sharp,P.M., McCutchan,F.E. and Hahn,B.H. (1995b) Recombination in HIV-1. Nature, 374, 124-126.
15. Salemi,M., De Oliveira,T., Courgnaud,V., Moulton,V., Holland,B., Cassol,S., Switzer,W.M. and Vandamme, A.-M. (2003) Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses. J. Virol., 77, 7202-7213.
16. Salminen,M.O., Carr,J.K., Burke,D.S. and McCutchan,F.E. (1995) Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses, 11, 1423-1425.
17. Suchard,M.A., Weiss,R.E., Dorman,K.S. and Sinsheimer,J.S. (2002) Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst Biol., 51, 715-728.
18. Worobey,M., Rambaut,A. and Holmes,E.C. (1999) Widespread intra-serotype recombination in natural populations of dengue virus. Proc. Natl Acad. Sci. USA, 96, 7352-7357.