Retrieval and classification are at the center of Music Information Retrieval research. Both tasks rely on a method to assess the similarity between two music documents. In the context of symbolically encoded melodies, pairwise alignment via dynamic programming has been the most widely used method. However, this approach fails to scale-up well in terms of time complexity and insufficiently models the variance between melodies of the same class. Compact representations and indexing techniques that capture the salient and robust properties of music content, are increasingly important. We adapt two existing bioinformatics tools to improve the melody retrieval and classification tasks. On two datasets of folk tunes and cover song melodies, we a...