Aligning Sequences to Compare Apples to Apples

• Before you can compare sequences, you need to make sure that you are comparing stretches of DNA that are evolutionarily related—i.e., that they are homologous sequences.
• Two sequences need to be aligned, so that related parts of sequences are lined up against each other and compared.

Comparing non-homologous sequences to determine evolutionary relationships among species is like comparing apples to oranges.