What reference management tool do you recommend?
There are several good reference management tools that are available. Some are freely available and some of them are subscription based. Each of these has their own advantages and drawbacks. You could try each of these and decide what is best for you before you start working on something as extensive as your Ph.D. thesis to avoid any inconvenience later. Even the subscription based softwares usually offer a free trial, which can help you evaluate if it works well for you, before you go ahead and make a purchase. Some of the popular reference management softwares are Mendeley, Zotero, EndNote, RefWorks, Bibdesk. Following is a short description of selected reference management tools.
Mendeley is a freely available reference management software. Additionally, it also functions as an academic social network that can help connect and collaborate with other researchers as well as a job search portal. Some of the key features of the referencing software include- automatic generation of bibliographies, easy import of papers from other softwares, ease of access both online as well as through iOS and android apps, ease of sharing reference database with other account holders. A drawback of this software is the limited availability which can be extended only after paying a fee.
Zotero is another freely available reference management software. The ease of access is similar to that of Mendeley, However, a distinguishing feature about Zotero is that it interacts efficiently and automatically with online resources by extracting and save complete bibliographic references even if you are just reading the paper/book.
EndNote is a subscription based reference management software. It helps you to search for references, find full text references in a click, automatically organizes your references as you work, provides feature to share and control access of you reference library, and ease of access through any device as other softwares.