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Logos
Logos Bible Study Platform is a powerful online Bible study tool. Links to the free edition can be found below (you will need to create a free account first).
E-Sword
E-sword is a fast and effective tool for Bible study. The basic software and resources are free, and more advanced resources are available for individual purchase.
Versions are available for PC, Mac, ipad, iphone and android.
Zotero
Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share research.
It is a stand-alone program which also connects to your web browser and your word processor.