Morphophonology (also morphophonemics or morphonology) is the branch of linguistics that studies the interaction between morphological and phonological or phonetic processes. Its chief focus is the sound changes that take place in morphemes (minimal meaningful units) when they combine to form words.
Morphophonological analysis often involves an attempt to give a series of formal rules that successfully predict the regular sound changes occurring in the morphemes of a given language. Such a series of rules converts a theoretical underlying representation into a surface form that is actually heard. The units of which the underlying representations of morphemes are composed are sometimes called morphophonemes. The surface form produced by the morphophonological rules may consist of phonemes (which are then subject to ordinary phonological rules to produce speech sounds or phones), or else the morphophonological analysis may bypass the phoneme stage and produce the phones itself.
When morphemes combine, they influence each other's sound structure (whether analyzed at a phonetic or phonemic level), resulting in different variant pronunciations for the same morpheme. Morphophonology attempts to analyze these processes. A language's morphophonological structure is generally described with a series of rules which, ideally, can predict every morphophonological alternation that takes place in the language.
An example of a morphophonological alternation in English is provided by the plural morpheme, written as "-s" or "-es". Its pronunciation alternates between [s], [z], and [ɪz], as in cats, dogs, and horses respectively. A purely phonological analysis would most likely assign to these three endings the phonemic representations /s/, /z/, /ɪz/. On a morphophonological level, however, they may all be considered to be forms of the underlying object //z//, which is a morphophoneme. The different forms it takes are dependent on the segment at the end of the morpheme to which it attaches: the dependencies are described by morphophonological rules. (The behaviour of the English past tense ending "-ed" is similar: it can be pronounced /t/, /d/ or /ɪd/, as in hoped, bobbed and added.)