The first two are viable commercial tests, the third is research only. The first detects the predominant sequence of the entire protease gene and the first two thirds of the reverse transcriptase.
Hybridization detects only a few specific drug related mutations.
Some investigators think that you really only need the info on the primary drug mutations. Others think you need to interpret those in the context of the whole sequence. The traditional assay uses the patients cells with HIV negative donor cells. It is fraught with many technical limitations, takes lots of time, is not very reproducible, and is primarily research only. This recombinant assay is incubated in a cell line, in the presence of HIV drugs.