This is typically done between string pairs, where a pronunciation is mapped to its spelling, an inflected form to its lemma, a spelling variant to its canonical spelling, or a name is transliterated from one alphabet into another.
many problems involve more than just two strings: • in morphology, the inflected forms of a (possibly irregular) verb are naturally considered together as a whole morphological paradigm in which different forms reinforce one another; • mapping an English word to its foreign transliteration may be easier when one considers the orthographic and phonological forms of both words; • similar cognates in multiple languages are naturally described together, in orthographic or phonological representations, or both; • modern and ancestral word forms form a phylogenetic tree in historical linguistics; • in bioinformatics and in system combination, multiple sequences need to be aligned in order to identify regions of similarity.