In this talk, I will discuss the dynamic programming methods for simultaneously predicting secondary structure and alignment for two sequences. This approach was first suggested by Sankoff in 1985. Recently, it has been implemented by several groups, using one or more heuristics to reduce the computational cost. Our implementation, Dynalign, finds the lowest free energy common secondary structure. It uses single sequence secondary structure prediction and sequence alignment data as input to reduce the search space to make the calculation tractable for long sequences.