Numerous methodologies have been proposed for DNA sequence similarity analysis, both alignment-based and alignment-free. Though alignment-based methods give accurate results, in the last few decades, AF methods have proven to come close to being as effective as AB methods while overcoming a lot of limitations. Our research revealed which methods provide greater performance independently and which have different combinations of possible methods. The feature representation has to be information lossless. Different representation methods are highlighted, and a second step of feature generation has been applied if the representation does not provide the required features for sequence comparison. We find that the k-mer analysis methods achieve higher accuracy than other approaches. k-mer analysis combined with matrix reduction yielded the highest accuracy, maintaining the lowest RF score among the different techniques.