Whether you’re a coding master or a total technophobe, a good text editor is a must-have for the molecular ecology toolkit.
Text editors are great for managing code, formatting input files, or jotting notes. But with so many different text editors to choose from (depending on your platform, your budget, and your skill set), how do you know which is right for you?
Here is an overview of the most popular text editors I’ve encountered in molecular ecology.
My review: Best simple editor for OS X
TextWrangler is a great all-purpose text editor that seems really popular in the molecular ecology world. It’s 100% free (free as in free speech and free beer) and easy to use. One feature I often use (accidentally) is its auto-saving cache; you can open TextWrangler, take a quick note during a meeting, and your note will still be there even if you restart the program without saving. If you like TextWrangler but are ready to graduate to something more advanced, you can also try BBEdit, which is made by the same developers.
Cons: Only available on OS X. May be too lightweight for programmers.
My review: Best simple editor for Windows
I’ll admit that I have never used this program, but Notepad ++ comes recommended by my officemate (@), who uses it for input file editing and some programming in python. Again, this is a popular, free, and easy-to-use option for your everyday molecular ecology needs.
Cons: Only available for Windows. May be too lightweight for programmers.
My review: Best all-around multi-platform tool
Sublime Text works on all operating systems and is loaded with some cool user-friendly features, including a powerful search shortcut feature and “distraction-free mode” (which I could definitely use). I’m also giving Sublime Text the award for best design – it’s a really beautiful environment to work in.
Cons: Sublime Text is a shareware, not freeware. You can download and test it free for as long as you like, but you have to pay $70 for a license (and you really should support the developers).
My review: Best editor for people who live on the command line
Ahh, Vim: a time-tested, cross-platform, fast and free text editor for programmers. I’ll be honest: I find it incredibly frustrating – but only because it has a steep learning curve that I haven’t invested enough time to learn! Vim is the de-factor Unix editor, which means that you can edit text in a remote environment via SSH (e.g., you university’s computer cluster). That alone is an incredibly important feature, and is why Vim earned a place on this list.
Cons: Steep learning curve.
Other TME-recommended Text Editors
Programmer’s Notepad comes recommended by @, who is the most celebrated bioinformatician at The Molecular Ecologist (based on number of posts in the How To… section). Arun says that this editor works great for programming, although it looks like it’s only available for Windows.
@ recommends jEdit, which is advertised as a “mature programmer’s text editor.” jEdit is written in java and appears to be user-friendly, plus there is a good collection of macros and plugins available to expand its capabilities.
@ recommends Atom, which is relatively new to the scene but is quickly becoming a popular tool. Atom is made by Github and has a minimalist core, but a huge number of open-source packages make it highly customizable.
Finally, some Text Editors that almost made the list include ICEcoder (a browser-based text editor), Brackets (a free product from Adobe), and Emacs (another time-tested and powerful editor with a steep learning curve).
Don’t see your favorite text editor on the list? Tell us about it in the comments!