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Nowadays, the term cover song (or simply cover) can mean any new version, performance, rendition, or recording of a previously recorded track. Cover song identification is a task that has received increased popularity in the Music Information Retrieval (MIR) community in recent years, as it provides a direct and objective way for evaluating music similarity. In this paper, we propose a new method for determining the similarity between tonal sequences and, therefore, for identifying cover songs. This is based on a novel chroma similarity measure, and on a newly developed dynamic programming local alignment technique. Results confirm that the performance of the proposed system is significantly superior to other state-of-the-art approaches (more than 57% better).