A (3+1)-dimensional generalized Yu–Toda–Sasa–Fukuyama equation is considered systematically. N-soliton solutions are obtained using Hirota’s bilinear method. The employment of the complex conjugate condition of parameters of N-soliton solutions leads to the construction of breather solutions. Then, the lump solution is obtained with the aid of the long-wave limit method. Based on the transformation mechanism of nonlinear waves, a series of nonlinear localized waves can be transformed from breathers, which include the quasi-kink soliton, M-shaped kink soliton, oscillation M-shaped kink soliton, multi-peak kink soliton, and quasi-periodic wave by analyzing the characteristic lines. Furthermore, the molecular state of the transformed two-breather is studied using velocity resonance, which is divided into three aspects, namely the modes of non-, semi-, and full transformation. The analytical method discussed in this paper can be further applied to the investigation of other complex high-dimensional nonlinear integrable systems.
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