13. The computer-based system of claim 9 , wherein the first electronic file is a modified version of the second electronic file.
9. A computer-implemented method for generating comparison output data indicating differences in annotations in electronic files, the method comprising: identifying a first annotation in a first electronic file; creating a first index for the first annotation, the first index including a plurality of words, pixels, rows, columns, or coordinates in the first electronic; creating a second index for a second electronic file different than the first electronic file, the second index including a plurality of words, pixels, rows, columns, or coordinates in the second electronic file; comparing, by the processor, the first index with the second index to determine whether the second electronic file contains a matching annotation having words, pixels, rows, columns, or coordinates corresponding to the first annotation; generating, based on the comparison, a matrix that identifies matches between the words, pixels, rows, columns, or coordinates in the first index of the first annotation and the second index of the second annotation; determining, based on the matrix of the comparison, whether the words, pixels, rows, columns, or coordinates in the first index of the first annotation are present in the second index of a second annotation in the second electronic file; and creating, by the processor and based on the determination, comparison output data including information for displaying a redline version of characters in the first annotation to indicate changes between the first annotation and the second annotation, wherein the processor inserts into the comparison output data a first hidden character marking a beginning of the redline version and a second hidden character marking an end of the redline version.