RFLP analysis
Restriction enzymes cleave DNA at very specific points. Many such enzymes are known, each cleaving at different recognition sites (nucleotide sequences).
These produce fragments of different lengths, which can be separated via gel electrophoresis, and hybridized to radioactive probes to determine where on the chloroplast genome they are located.
Maps of the restriction sites are then constructed. We can detect numerous kinds of changes including point mutations, inversions, and deletions.
These can be used in cladistic analyses. e.g. Asteraceae