10. A computer-implemented method for generating comparison output files indicating differences in annotations, the method comprising: create a first index for a first electronic file; identifying, by a processor, hidden characters for an insertion point and an end point of a first annotation in the first electronic file; identifying a first portion of the first index between the identified hidden characters; creating a second index for a second electronic file different than the first electronic file; comparing, by the processor, the identified first portion with the second electronic file, to determine whether the second electronic file contains a matching annotation corresponding to the first annotation; and generating, by the processor and based on the comparison, a comparison output file including information for displaying a modified appearance of characters in the first annotation to indicate that the second electronic file does not contain a matching annotation.
12. The computer-implemented method of claim 10 , further comprising: identifying, by the processor, a first annotation location corresponding to the first annotation; identifying, by the processor, a second annotation location corresponding to a second annotation in the second electronic file; creating, by the processor, an annotation index including the first annotation location and the second annotation location; determining based on the annotation index, by the processor, whether the second annotation is a matching annotation corresponding to the first annotation.