JabRef is a graphical application for managing bibliographical databases. JabRef is designed specifically for BibTeX bases, but can import and export many other bibliographic formats. JabRef runs on all platforms and requires Java 1.5 or newer.
We use it all the time at work to manage 1000s of references. Many thanks to the team who keep maintaining and improving JabRef.
The only reference manager that has a hierarchical group-tree for the classification of the references.
JabRef + Zotero is my ultimate bibliography management duo.
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