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The two-phase 3D jet spatial instability tool (2PJIT) is a generalized Matlab-based software used to predict the growth of instabilities in two-phase shear flows involving cylindrical jets. The software solves the Linearized Navier–Stokes equation via the Chebyshev spectral method in both the liquid and gas phase along with the interfacial constraints. For a given set of input frequencies, the software outputs the corresponding wavenumbers, the associated eigen-vector/function, and the spatial growth rate for radial, azimuthal, and axial disturbances.