just as in cancer or other infectious diseases, the natural selection placed on the hiv population within the patient by therapy (haart) will make it likely for the emergence of drug-resistant strains. thus, even patients who do not have drug-resistant strains of hiv will benefit if this therapy is a success.

of course, one cannot be sure that the selection pressure exerted by the t-cells with the ccr5 (\delta 32?) deletion will not result in hiv strains capable of invading t-cells via a new mechanism.

there are tools to help parallelize code:
http://www.stats.uwo.ca/faculty/yu/Rmpi/
http://www.sfu.ca/~sblay/R/snow.html

i agree with you that the post above is not insightful; however, i will disagree that humans have a higher mutation rate than e.coli. humans have much more accurate error correction machinery than bacteria.

http://www.genetics.org/cgi/content/full/156/1/297

however, the previous post is not insightful for a multitude of reasons. the crucial error is that the anonymous coward is not taking into account various evolutionary forces. the citrate mutation could have appeared and disappeared by chance (genetic drift) multiple times if the citrate metabolism gene did not confer enough of an advantage (generally it has to be s > 1/N, where s is the advantage and N is the population). so the simple arithmetic while adorable, is deeply ignorant. to edify, get this from your library...

http://www.amazon.com/Population-Genetics-John-H-Gillespie/dp/0801880084/