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Perseus is a massive digital library, whose "flagship collection, under development since 1987, covers the history, literature and culture of the Greco-Roman world." You can read & search in English, Greek, & Latin. It's the online academic gold-standard.
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This is the easiest place to access primary sources for NT studies, (from the 1st-3rd centuries C.E.). Covering the NT, Apocrypha, Gnostic Lit, Church Fathers, sources are arranged by date and by type.
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"Early Jewish Writings is the most complete collection of Jewish documents from antiquity with translations, introductions, and links." This is Peter Kirby's easy-to-navigate collections of Josephus, Philo, the Pseudepigrapha, Deuterocanon.
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One of the links from Michael Marlowe's "Bible Research" website, this page contains an excellent selection of online Greek NT's, Lexicons, and sundry Greek-related topics.
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This is Joel Kavlesmaski's page on the Septuagint. Although most of the links are to places where you can purchase the Septuagint, this site is a particularly helpful place to become conversant in Septuagint studies.
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Completed in 2007 & published by Oxford University Press, this is the official free, online version of the English translation of the Septuagint.
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This site contains the Greek text of the Septuagint. Hovering over a word will show its parsing information, but not its translation.
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CCEL hosts "hundreds of classic Christian books selected for edification and education." While the earliest texts on the site are the Epistle of Barnabas & Irenaeus' letters, the site consists mostly of authors from the 1100's onwards.
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"An online resource dedicated to the Gospel of Thomas other early [non-canonical] Christian Gospels." Not only does the site give you information, but provides links to online texts for each gospel.
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Translated by Rabbi Dr. I. Epstein, this contains most of the Babylonian Talmud.
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This site contains both primary and secondary sources on Medieval Christian Spirituality, and is an excellent place to begin your research.
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This is the onilne Greek-Latin/French/English text of Codex Bezae Cantabrigiensis (D 05). Although the webpage is in French, a parallel Greek-English is available.
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This is Daniel C. Stevenson's site where users can "select from a list of 441 works of classical literature by 59 different authors, including user-driven commentary and 'reader's choice' Web sites."
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There are many good places to start research on the DSS. This site, hosted at ibiblio.org, is part of an exhibition at the Library of Congress in Washington DC. It's a very good primer that equips you for further research.
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The Vatican is digitizing its library!
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