We study the cooperative optical coupling between regularly spaced atoms in a one-dimensional waveguide using decompositions to subradiant and superradiant collective excitation eigenmodes, direct numerical solutions, and analytical transfer-matrix methods. We illustrate how the spectrum of transmitted light through the waveguide including the emergence of narrow Fano resonances can be understood by the resonance features of the eigenmodes. We describe a method based on superradiant and subradiant modes to engineer the optical response of the waveguide and to store light. The stopping of light is obtained by transferring an atomic excitation to a subradiant collective mode with the zero radiative resonance linewidth by controlling the level shift of an atom in the waveguide. Moreover, we obtain an exact analytic solution for the transmitted light through the waveguide for the case of a regular lattice of atoms and provide a simple description how the light transmission may present large resonance shifts when the lattice spacing is close, but not exactly equal, to half of the wavelength of the light. Experimental imperfections such as fluctuations of the positions of the atoms and loss of light from the waveguide are easily quantified in the numerical simulations, which produce the natural result that the optical response of the atomic array tends toward the response of a gas with random atomic positions.