A method is provided for content alignment. The method includes obtaining a first content sequence and a second content sequence different from the first content sequence. The method also includes representing each of the first content sequence and the second content sequence in a hierarchical structure containing an ordered root element sequence and a sub-tree structure. The ordered root element sequence includes a plurality of root elements and each root element is associated with a sub-tree of elements. The method also includes determining a desired alignment between the first content sequence and the second content sequence using dynamic programming, and outputting results of the desired alignment between the first content sequence and the second content sequence.