Restriction site advantages

Although distance methods have certain advantages for the analysis of restriction site data, notably their computational efficiency, they also have an important disadvantage. By reducing the data to pairwise distances, important information on the evolutionary history of individual restriction sites is lost. In chloroplast DNA, for example, individual sites often evolve at very different rates. A parsimony analysis of 328 restriction site mutations shared among two or more taxa in a survey of 57 taxa from the sunflower family showed that 186 of the sites had only a single mutation, whereas 6 sites showed nine or more mutations.24 A conservative statistical... 

The main advantages of RFLP analysis are that it is simple to develop and use. It also does not require expensive equipment, and it is effective for genotypingasmall number of samples. The principle disadvantages are that it is time consuming, labor intensive, and not amenable for large numbers of samples or genotypes. Another drawback is that not all SNPs produce a usable restriction site. 

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