Alignment-free sequence analysis

Alignment-free sequence analysis is a way of studying the similarities and differences between DNA and protein sequences without using an alignment. Algorithms look at individual characters (or "letters") in the sequences and count how many times each one appears. They also look at sequences of more than one character, and compare them to one another. By seeing which sequences are alike and which ones are different, it can tell us something about the relationship between the sequences (for example, similar sequences probably belong to similar organisms).