Advice for Aspiring Phylogeneticists

Ironically, the most advanced programs often require the simplest input: ASCII text files unadulterated by superfluous code, or hiding invisible extensions. The best way to do this is to never use an advanced Word processor such as Microsoft Office or Mac Pages. Don’t even use the simpler text editors that were included in the base install of your operating system (e.g., TextEdit in Mac OSX or Notepad in Windows). Go straight to the internet and download either TextWrangler (Mac OSX) or TextPad (Windows). Use these programs to create, edit, revise, and review all of the text files that will be input to or output from advanced applications. In addition to sparing you the unbelievable amount of confusion that can result from hidden formatting, these programs are wonderfully easy to use and full of useful features (try, for example, using the option key to select columns of text in TextWrangler).

We all love programs with beautiful graphical user interfaces (GUIs). We should all use a few moments of the time these interfaces have saved us to thank the developers who have used many hours of their own time to develop them. For brand-new and highly specialized analyses, however, developers have ample justification for making their methods available only in the form of somewhat-more-difficult-to-use command line applications. If you are going to do phylogenetics right, you must learn to use these applications. Early in this process, you should do yourself a favor and learn the basics of UNIX syntax and file architecture. As a user, this can make you more efficient in the long run. Many command line applications can be embedded in workflows allowing easy repeated analyses. Some programs with GUIs can't be automated in this way. The first time you dig through menus to delete a taxon, it may seem convenient to be able to poke around and do this. The hundredth time, you probably want to just type "del 3" instead.

If you’re going to do modern phylogenetic analyses you are going to be learning new programs. All the time. Some programs are not easy to use. Some take weeks, months, or even years to master. You cannot allow this to lead you on a detour of convenience to use of inappropriate analyses. It is your responsibility as a scientist to do the best analyses possible. Don’t be lazy: when you stop learning new programs you stop doing modern phylogenetics. After you've learned a new program, come back to this site and post a tutorial to help your fellow phylogeneticists.

One surprisingly common impediment to progress is the reluctance of end-users to seek support, or their inability to get this support when its needed. One problem is that developers tend to get unresponsive (or annoyed) when consumers of their applications are constantly asking them questions that are mundane or naive. To a degree, this is reasonable. These people have already put a ton of time into helping you, and are justified in recoiling if you seem unwilling to put the same time into helping yourself. As a matter of respect, you should read over the instructions and try some basic trouble shooting on your own before asking the developer for help directly. We don’t learn programs with someone holding our hand, we learn them primarily through experimentation, trial, and error. Having said this, of course, some developers may deserve a bit of hassling if they haven’t taken even the most basic measures to make their software accessible to the public. Moreover, its important to remember that most developers are your colleagues and are eager to communicate with informed users of their applications. They’re even hoping for your help spreading their methods, extending their application, and catching bugs. Developers also (generally) appreciate detailed error reports and emails of files that consistently reproduce an error. You're much more likely to get help this way (and developers aren't going to "steal" the file you send them and publish it, which is a concern some users seem to have).

Consider reading this to help understand how developers like to see questions structured. Providing details (like program and error output) will help you get answers from developers and mailing lists quicker.

Reconstructing phylogenetic trees is one of the most challenging problems in biology (under many optimization criteria, it's part of a class of extremely hard problems). You are not going to learn how phylogenetic algorithms work and implement them in a single afternoon. This has led many people to use relatively simple methods that are available in easy-to-use programs. Don’t fall into this trap.