(This review will be updated in the future as I learn the ins-and-outs of the program.) DSS will be used throughout for Dead Sea Scroll(s).
The Dead Sea Scrolls Electronic Library is your next level of discovery. This program was developed by scholars to fully study the NON-Biblical scrolls. I stress "non-Biblical scrolls" because the biblical scrolls will likely be added in the forthcoming editions to this electronic project. This program does contain the same searchable features for the Leningrad Codex B19^A (The most popular masoretic Hebrew text of the Tanach/Old Testament). In other words the Biblical text that the program uses for comparison is not the DSS.
Features: You can search for any Semitic root(Hebrew/Aramaic) as well as grammatical structures, and complete phrases. You can parallel a reading of the DSS with its translation. You can maintain window tabs for quick selection between actual photographs of the DSS, the text in standard Hebrew font, the translation, a Hebrew Bible, and your notes (plus various other tools). The indistinguishable letters are marked with a graded scale based on confidence of choice. The grammatical catergories are also relative to the scholar(s) opinion because vowels points were absent in the original DSS.
I just started using the program. If you are not comfortable navigating computers it may be a challenge to use at the start. The user interface is a little bit primitive compared to modern Windows programs.
All of this is contained on one CD. You can install the program to run with the CD (14MB? disk space) or run without the CD (600+MB disk space).
If you have any questions, post them in the COMMENTS to this review and I will attempt to answer them.