Notes on pairwise alignment with dynamic programming

This informal note introduces important literatures on pairwise biological sequence alignment with dynamic programming (DP), disambiguates a few different formulations, investigates the choice of gap cost function and discusses the implementation of DP-based alignment with a focus on practical applications. It targets developers who are interested in the history of DP-based alignment and want to understand it in depth. Importantly, this note is not a general tutorial. Audience should be familiar with the basis of pairwise alignment before reading the note.