In this paper a methodology for the alignment of waves in the photoplethysmography (PPG) register signal is shown. The procedure uses algorithms for dynamic programming and for optimization in order to generate a single segmentation of these waves in the PPG signal and the individual reconstruction of each wave. By aligning a pattern signal for the photoplethysmography, it is possible to make an individual segmentation of waves present in the PPG signal. Once the reconstruction of each individual wave is obtained, these data are indexed in an array, which enables easier temporary markers such as the individual location of each peak to the signal wave analysis.