Special Interest Data Set 2:
Swedish Transmission Chain

Study of 11 Swedish patients with a known transmission chain.

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

Leitner T, Escanilla D, Franzén C, Uhlén 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

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.

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