Multiple-changepoint testing for an alternating segments model of a binarysequence

A binary sequence may give the appearance of being composed of alternating segments with relatively high and relatively low probability of success. De termining whether such an alternating pattern is significant is a multiple- changepoint problem where the number of segments and their success probabil ities are unknown, with the added constraint of segment alternation. A dyna mic programming method for determining the optimal segmentation into a give n number of segments is provided. Given this, a variation on the simulation method of Venter and Steel (1996, Computational Statistics and Data Analys is 22, 481-504) may be employed to test the null hypothesis of a homogeneou s sequence as well as to estimate the number and location of changepoints. A sample application, the assessment of the possibility of genetic recombin ation in HIV sequences, is presented.