Some references

Observation (dating from 31/08): This bibliography is not complete. All participants are quite welcome to send me other references should they wish to (or pointers to programs or web pages). Just send them to me at the address: sagot@pasteur.fr. Thanks in advance.

Charleston M. A. (1998) Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149:191-223.

Duret L. and Mouchiroud D. (1999) Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate Mol. Biol. Evol. (in press).

Gao F., Bailes E., Robertson D. L., Chen Y., Rodenburg C. M., Michael S. F., Cummins L. B., Arthur I. O., Peeters M., Shaw G., Sharp P. M., Hahn B. H. (1999) Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397:436-440

Gao F., Yue L., White A. T., Pappas P. G., Barchue J., Hanson A. P., Greene B. M., Sharp P. M., Shaw G. M., Hahn B. H. (1992) Human infection by genetically diverse SIVsm-related HIV-2 in West Africa. Nature 358:495-499.

Gascuel O., Jean-Marie A. (1999) Classification par arbre : la forme de l'arbre inféré dépend du schéma algorithmique retenu. Actes des rencontres de la Société Francophone de Classification, Nancy, Septembre 1999.

Harvey P. H., Leigh Brown A. J., Maynard Smith J. and Nee S. (eds.) (1996) New Uses for New Phylogenies. Oxford University Press.

Huet T., Chenyier R., Meyerhans A., Roelants G., Wain-Hobson S. (1990) Genetic organization of a chimpanzee lentivirus related to HIV-1. Nature 345:356-358.

Janssens W., Fransen K., Peeters M., Heyndrickx L., Motte J., Bedjabaga L., Delaporte E., Piot P., van der Groen G. (1994) Phylogenetic analysis of a new chimpanzee lentivirus SIVcpz-gab2 from a wild-captured chimpanzee from Gabon. AIDS Res. & Hum Retroviruses 10:1191-1192.

Jin M. J., Hui H., Robertson D. L., Müller M. C., Barré-Sinoussi F., Hirsch V. M., Allan J. S., Shaw G. M., Sharp P. M., Hahn B. H. (1994) Mosaic genome structure of simian immunodeficiency virus from West African monkeys. EMBO J. 13:2935-2947.

Mouchiroud D., Robinson M., Gautier C. (1997) Impact of changes in GC content on the silent molecular clock in murids. Gene 205(1-2):317-22. x

Mouchiroud D., Gautier C., Bernardi G. (1995) Frequencies of synonymous substitutions in mammals are gene-specific and correlated with frequencies of nonsynonymous substitutions. J. Mol. Evol. 40(1):107-13.

Page R. D. M. and Charleston M. A. (1997) Reconciled trees and incongruent gene and species trees. In Proceedings of the DIMACS workshop on Mathematical Hierarchies and Biology, Mirkin B., McMorris F. R., Roberts F. S. and Rzhetsky A. (eds), DIMACS series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society,

Page R. D. M. (1994) Parallel phylogenies: Reconstructing the history of host-parasite assemblages. Cladistics 10:155-173.

Peeters M., Honore C., Huet T., Bedjabaga L., Ossari S., Bussi P., Cooper R. W., Delaporte E. (1989) Isolation and partial characterization of an HIV - related virus occurring naturally in chimpanzees in Gabon. AIDS 3:625-630.

Simon F., Mauclère P., Roques P., I. Loussert-Ajaka, Müller-Trutwin M. C., Saragosti S., Georges-Courbot M.-C., Barré-Sinoussi F., Brun-Vézinet F. (1998) Identification of a new human Immunodeficiency virus type 1 distinct from group M and group O. Nature Medicine 4:1032-1037.

Zhu T., Korber B. T., Nahmias A. J., Hooper E., Sharp P. M., Ho D. D. (1998) An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 391:594-597.



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