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HIV sequence database



Special Interest Data Set 2:
Swedish Transmission Chain

Description

Study of 11 Swedish patients with a known transmission chain.

Data

Alignment - env 13 sequences
Alignment - gag 13 sequences
Tree file Tree of the true transmission history
Clinical data CSV file

Primary reference

Leitner T, Escanilla D, Franzen C, Uhlen M, Albert J. Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis.
Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10864-9.
PMID 8855273

Additional studies that used these data

Leitner T, Kumar S, Albert J. Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history.
J Virol. 1997 Jun;71(6):4761-70.
PMID 9151870

Leitner T, Albert J. The molecular clock of HIV-1 unveiled through analysis of a known transmission history.
Proc Natl Acad Sci U S A. 1999 Sep 14;96(19):10752-7.
PMID 10485898

Leitner T, Fitch, WM 1999. The phylogenetics of known transmission histories.
Pp. 315-345 in K. A. Crandall, ed. The evolution of HIV. Johns Hopkins University Press, Baltimore, Md.

Yang, Z, Nielsen, R, Goldman, N, Krabbe Pedersen, A-M. Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites.
Genetics. 2000 May;155(1):431-49.
PMID 10790415

Seo, TK, Thorne, JL, Hasegawa, M, Kishino, H. A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times.
Bioinformatics. 2002 Jan;18(1):115-23.
PMID 11836219

Jenkins, GM, Rambaut, A, Pybus, OG, Holmes, EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis.
J Mol Evol. 2002 Feb;54(2):156-65.
PMID 11821909

Kosakovsky Pond SL, Frost, SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection.
Mol Biol Evol. 2005 May;22(5):1208-22.
PMID 15703242

Nickle, DC, Heath, L, Jensen, MA, Gilbert, PB, Mullins, JI, Kosakovsky Pond, SL. HIV-Specific Probabilistic Models of Protein Evolution.
PLoS ONE. 2007 Jun 6;2(6):e503.
PMID 17551583

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last modified: Tue Sep 13 09:33 2011


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