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Sefaria: a Living Library of Jewish Texts Online
Sefaria is home to 3,000 years of Jewish texts providing access to texts, translations, and commentaries for the ongoing study of Torah.  
Introduction to the Talmud and Midrash (1996) 
by Strack, Hermann L. and Stemberger, Gunter
The Babylonian Talmud, Complete with Spanish Bookmarks
The Jerusalem Talmud (2nd Order), Moed, Shabbat-Eruvin (by Guggenheimer)
The Jerusalem Talmud (4th Order), Neziqin_Bava_Qamma_Mesia_Batra
The Jerusalem Talmud (4th Order), Neziqin_Sheviit_Avodah_Zarah
The Mishna (1993), by Danby,H, translated from the Hebrew with brief notes
The Book of Legends/Sefer Ha-Aggadah: Legends from the Talmud
and the Midrash , By Bialik, H and Hana Ravnitzky, Y (Ed.)
The New Testament and the Mishna: Cross Reference Index , By Gianotti
The Works of Josephus Complete and Unabridged, F.Josephus and W. Whiston (1987)
Flavius Josephus Interpretation and History, By Brill (2011)
Genesis and the Jewish Antiquities of Flavius Josephus, T. Franxman (1979)
JOSEPHUS, FLAVIUS Link on Jewish Encyclopedia
Josephus on Samaritan Origins Link on University of Arizona
The Origin of the Samaritans, by Kartveit,M (2009)
 The Samaritans and Early Judaism A Literary Analysis, by Hjelm,I (2000)
The History of the Second Temple Period, by Sacchi,P (2000)
The Digital Dead Sea Scrolls Online link at Israel Museum 
The Leon Levy Dead Sea Scrolls Digital Library Online link at Israel Antiquities
The Dead Sea Scrolls | The Israel Museum, Jerusalem Online link
With Letters of Light_ Studies in the Dead Sea Scrolls, Early Jewish Apocalypticism, Magic, by Arbel and Orlov (2011)