Reference manager round-up: alternatives to EndNote

written by John Borghi

Whether your desk is piled high with printed articles, or your computer desktop is filled with incongruously named PDFs, unmanaged references can be a headache even when you aren’t desperately trying to locate an article for your advisor, or finish a grant proposal at the absolute last minute. Using a piece of reference management software is one of the easiest ways to alleviate this headache. Unfortunately, not all reference managers are created equal. Choosing the right program can make the research process easier and much more efficient. Choosing the wrong manager can generate a whole new set of headaches.

The de facto standard for reference management is EndNote. Now on its seventeenth version, Endnote has been widely adopted by researchers and academic libraries alike. Unfortunately, Endnote is also inordinately costly, difficult to use, and lacks some of the basic tools available in more cost effective, or even free, options. Luckily there are lots of alternatives.

Because many alternatives to Endnote share a common set of tools for generating references: inserting citations into text, syncing, and sharing PDFs, choosing the right options depends on the needs of the individual researcher. Some options are designed to managing extensive libraries of PDFs, others are designed to generate references on the fly from the results of literature or web searches, and still others are designed to facilitate collaboration and communication. No matter what you’re looking for in a reference manager, there is an option out there for you- and it isn’t EndNote.

paper picture
Photo courtesy Jenni C

Free to use Programs:


Developer: Colwiz
Supports: Windows, Mac OSX, Linux
Mobile Support: iPhone, iPad, Android
Integration with word processing software: Yes
Web-Importer Support: All browsers

Colwiz is designed to both organize references and facilitate collaboration. Like other reference management tools, Colwiz can automatically generate both in-text citations and full bibliographies from downloaded references, and can integrate (via a free plug-in) with most word processing software. In keeping with its focus on collaboration, Colwiz includes tools for sharing both articles and user generated comments. Uniquely, Colwiz also allows users to share and manage calendars and project checklists.

Colwiz currently has an extensive set of analytic tools, allowing users to track connections between authors, journals, and subject areas references. Like other free software, Colwiz includes a limited amount of free online storage space (2 GB) for backing up and syncing references between collaborators and devices. What Colwiz has in terms of analytic and collaboration tools, it lacks in library management. Unlike options such as Mendeley or Papers, Colwiz currently lacks tools for renaming and managing directories of reference files.

Advantages: Extensive collaborative and analytic features,
Disadvantages: Less extensive library organization tools


Developer: Docear
Supports: Windows, Mac OSX, Linux
Mobile Support: None
Integration with word processing software: Yes
Web-Importer Support: None

Though it shares many features with other reference management options, Docear has a unique system for organizing information. Unlike options that display references as lists of citations or annotations, Docear utilizes a “mind map” that allows users to efficiently map the connections between references and quickly prepare outlines.

Like other reference management tools, Docear allows users to automatically generate citations from downloaded references. However, at present, it does not integrate with word processing software. Docear allows users to share both references and annotations, including bookmarks and comments. Because Docear is still in beta, the user interface can be clunky and less intuitive than other options.

Advantages: Unique “mind map” organization
Disadvantages: Clunky interface


Developer: Elsevier
Supports: Windows, Mac OSX, Linux
Mobile Support: iPhone, iPad
Integration with word processing software: Yes
Web-Importer Support: All browsers

Mendeley is also designed to both organize references and facilitate collaboration. Along with the standard tools for automatically generating citations (both in-text and full bibliographies) from downloaded references and integration with most word processing software, Mendeley has some additional limited networking and analytic tools.

Of all the free options, Mendeley has arguably the best tools for library management, including tools for automatically naming and organizing PDF files. In addition, Mendeley offers users a limited amount of free online storage space (2 GB) for backing up and syncing references between collaborators and devices. Though Mendeley offers some tools for exploring the connections between authors and publications, it does not offer the same degree of analytics as other options.

Advantages: Intuitive library management tools
Disadvantages: Less extensive analytics than other options


Developer: Labtiva
Supports: Windows, Mac OSX
Mobile Support: None
Integration with word processing software: No
Web-Importer Support: All browsers

Touted as a replacement for Nature’s now defunct Connotea software, ReadCube allows users to automatically generate citations and bibliographies. When available, ReadCube also supports enhanced views of articles in PDF format- including integrated author information, interactive references, and direct access to article supplements. Though it currently does not support direct integration with word processing software, ReadCube includes an option to automatically export references to EndNote. Because of its ties to major publishing companies, ReadCube can also provide users with article recommendations based on the contents of their libraries.

Advantages: Enhanced PDF reader, article recommendations
Disadvantages: Lack of direct integration with word processing software



Developer: George Mason University
Supports: Windows, Mac OSX, Linux
Mobile Support: iPhone, iPad, Android
Integration with word processing software: Yes
Web-Importer Support: Firefox, Chrome

Formerly an add-on for Firefox, Zotero now includes both a stand-alone program and an add-on that adds functionality to every major web browser. When used in conjunction with library catalogs and search engines, Zotero allows users to save references and full text PDFs directly to their libraries. As with other options, saved references can be exported as both in-text citations and bibliographies.

Like other options, Zotero provides some free online space for backing up and syncing references between devices. However, the amount of space is significantly smaller than other options (300 MB). Similar to other options, Zotero integrates with a variety of word processing software and has some limited tools for sharing information with collaborators.

Advantages: Ability to save references directly from web and database searches
Disadvantages: Current version has difficulty managing large libraries

Pay to use Programs:


Developer: Mekentosj/Springer
Supports: Windows, Mac OSX
Mobile Support: iPhone, iPad
Magic Citation Support: Almost every program
Price: $79.00, $49.00 (Student license)

Developed by a pair of biology PhD candidates to manage their burgeoning collection of PDFs, Papers has several features that make it a powerful tool for reference management. Like many other options (except Endnote), Papers automatically generates citations (both bibliographies and in-text citations) from downloaded publications and citations. With its “Magic Citations” option, Papers can be used to insert citation information into text generated in almost any program imaginable.

Significantly cheaper than EndNote, Papers offers better technical support and more online features. Though it has a similar interface and many of the same organizational tools as several of the free options, Papers offers probably the most robust tools for integrating citations into manuscripts as they are being written.

Advantages: “Magic Citations” is very smooth and easy to use.
Disadvantages: Occasionally runs into difficulty when extracting meta-data from PDF files.


Developer: ProQuest
Supports: OS Independent
Mobile Support: iPhone, iPad
Browser Support: All
Price: $100

RefWorks is an online platform for managing references, collaborating, and writing. Because it lives completely on the web, users can access their libraries from any web-connected computer. Though it boasts some decent online style guides, RefWorks does not automatically generate citations as easily as other options. RefWorks also does not allow users with an individual license to attach files (including PDFs) to their reference lists. Similarly, while it can import reference information from online databases, RefWorks currently cannot import metadata from PDF files. Despite this relative lack of features, RefWorks is quite costly (licenses run about $100 per year).

Advantages: Accessible from any device
Disadvantages: Missing many features found in free options.

And if you absolutely have to…


Developer: Thomson Reuters
Supports: Windows, Mac OSX
Mobile Support: iPhone, iPad
Web Version Support: All browsers
Price: $249.95, $113.95 (Student license)

EndNote’s biggest (and maybe only) strength is its momentum. Researchers accustomed to creating bibliographies and managing in-text citations using EndNote may find it challenging to switch to other software. Unfortunately, for new users, EndNote has quite a steep learning curve.

The initial cost of Endnote is high and an annual license renewal is required. Despite this cost, Endnote lacks several features included in other software. For example, it does not easily support automatic generation of citations from PDF files and has very limited tools for collaborating with other researchers. Endnote does have a decent level of technical support and comes with online features more comprehensive than some of the less costly options. These features, however, do not overcome the fact that other options do everything EndNote does- but cheaper and better. If you insist on using EndNote, the web version is free and slightly more user friendly than the standalone version.

Advantages: Broad institutional support
Disadvantages: Very pricey, clunky user interface, relatively unintuitive


Research always involves headaches and last minute scrambles. Using the right reference manager will help you reduce those precarious stacks of articles and clear your desktop of icons. The right reference manager won’t make research easier, but may make the process more efficient.

The table below maps the software reviewed in this article to particular reference management needs. Options that cost money generally come with a thirty day trial, so it’s worth testing several until you find the one that works best for you.



I want to:

I should use:

Generate citations and bibliographies in different styles

Colwiz, Mendeley, ReadCube, Zotero, (Begrudgingly: EndNote)

Import references from online databases

Colwiz, Mendeley, Zotero, Papers

Synch my references across all my devices

Colwiz, Mendeley, Zotero, Papers

Share references with collaborators

Colwiz, Mendeley, Zotero, Papers, Refworks

Insert in-text citations in word processing documents

Mendeley, Zotero, Papers

Generate an organized library of PDF files

Mendeley, Papers

Archive results of web searches


Access content of enhanced PDF files



Do you use a reference management tool ? How has it affected your research or writing process? Do you have a particular preference (even if it is EndNote)? Please leave a comment below.







8 thoughts on “Reference manager round-up: alternatives to EndNote”

  • I’ve recently switched from EndNote to Zotero (as a PC/Android user) and been very pleased. One thing to note–Zotero does have the capability to rename and organize pdf files with a plugin from a guy at Columbia.

    ZotFile is pretty awesome in that you can also set up a syncing system for sending and fetching annotated pdf’s from a tablet.

    And you can set Zotero/ZotFile to store your pdf’s in a Dropbox folder to avoid space limitations and have cross-computer, cross-platform access.

    • Thanks for the comment. I hadn’t heard of ZotFile. The number and variety of plugins is really a strength of Zotero (

      There are a lot of nice ways around the free space limitations. When I was writing my thesis I backed up my Mendeley library in my Google Drive- which had the added benefit of making it quite simple to send large numbers of papers to my adviser.

  • The Colwiz installer disk image for Mac OSX crashes the Finder in the latest version of the OS 10.9 (Mavericks) and consequently can’t be installed. Looks promising none the less.

    • I tested Colwiz on Windows 7 and Mountain Lion and it worked well on both. I’m sorry to hear that it breaks down on Mavericks. Compatibility issues aside, it is a nice piece of software. Mendeley is quite similar and shares some of the same collaboration tools (though to a lesser degree), so it might be worth checking that out of Colwiz is being difficult.

  • Hi John, Thanks for a great analysis. My biggest problem with most of these solutions is that they have limited ability to actually cite correctly for the full range of information sources that academics use in their writing (which is why I gave up on using EndNote when I wrote my dissertation). The integration with Word (an archaic writing product) is also problematic, especially if writing a long piece like a dissertation.
    As a result, I have now developed a new product: writing+referencing all-in-one using pre-defined styles (text+cites+bib). It is cloud-based, and we have just released the Beta version at I’d be grateful if you took a look, if you have the time. It is not as advanced as some of the other referencing software, at this stage, but we have plans, for example, to bring the library databases online. But, the writing side, is very nice indeed (especially if you like consitent formatting).
    cheers, Linda

    • Thanks for the comment. I think there is probably another post to be written about modern writing programs. After losing an early draft due to a hard drive failure, I wrote my PhD thesis in Google Docs. It wasn’t the worst thing in the world, but I would definitely be interested in exploring other options.

  • Hi John, this is a nice round-up! It’s nice to have a condensed, up-to-date view of what’s available.

    One thing that feature-based lists often fail to encapsulate is the ease of use / “comfort factor” that can vary widely between different programs. I think many people would agree that Endnote isn’t exactly intuitive, but how about Zotero vs. Mendeley? Mendeley has had a team of ~20 full-time engineers dedicated to its development over the past several years, while Zotero has only ever had one or two full-time developers (with a wider community of volunteers).

    This can lead to a huge difference in consistency and usability between the two, which doesn’t show through when merely listing features. To get a feel for these slightly intangible differences, it would be great to see comments from users who have evaluated each of the alternatives, e.g. why it worked for them or why not.

    For our part at Paperpile (, we’ve developed a feature-rich reference manager with a small team, allowing us to pay attention to the small details that make users’ lives easier. Paperpile isn’t free ($36/year), but it’s the only Endnote alternative featuring Google Drive integration and citation formatting in Google Docs. It may not stand out in a feature-list comparison, but anyone looking for an easy to use Endnote alternative may be interested in giving it a try.

    • Hi Greg,

      Thanks for the comment. I your point about the “comfort factor” is a really good one. I generally encourage people to try several options before making a decision.

      I think Mendeley and Zotero are actually pretty equal in terms of their ease of use. I’ve used Mendeley for 3-4 years(both as a research scientist and now as a science informationist) and the Zotero desktop client feels very similar. Overall, I think Papers is probably the most intuitive option available- I just wasn’t ready to pay for it when I was a grad student.

Leave a Reply to Linda Glassop Cancel reply