论文软件

Docear
免费软件。Docear的优点是可以自动提取PDF中的highlight，并且整合了开源思维导图软件。开发的起初就是为了写博士论文，通过文献阅读和管理，生成思维导图，从而直接用来写博士论文。
可以将PDF中的标注和PDF与论文章节相关联

Citavi
可以将PDF中的标注和PDF与论文章节相关联
免费版只支持100条文献内容

Qiqqa
支持在windows系统上在指定文件夹的PDF中进行搜索

DEVONthink Pro Office
支持在Mac系统上在指定文件夹的PDF中进行搜索

Histcite
Histcite 是一款文献引文分析工具，通过数据分析，可以快速绘制出某个研究领域的发展脉络图，让你找到重要文献和学术大牛。

Zotero
免费的文献管理程序，安装ZotFile后，可以手动(无法自动)提取PDF中的标注内容，但是无法将标注内容与论文章节进行关联。
可以和Dropbox整合，进行同步

Sente
This feature is also available in Sente. The idea is: you quote a certain sentence or paragraph from the PDF; then, give a title which summarizes the core point of the quote and tag it if you want to. These quotes serve as a short summary of the article. The titles are your reminds of the core points of the quote. It is like summarizing the summary. Very neat approach to reading articles. The neat part in Sente is each of these short quotes could be exported as a separate note file. That means, if you have 20 quotations from the article, you will have 20 short notes: titled appropriately in a folder in finder.