Advice for the aspiring phylogeneticist: Part II

Don’t be intimidated by command line only applications. We all love programs with beautiful graphical user interfaces (GUIs). We should all use a few moments of the time these interfaces have save us to thank the developers who have used many hours of their own time to develop them. For brand-new and highly specialized analyses, developers are justified in making their methods available only in the form of somewhat-more-difficult-to-use text-based analyses. If you are going to do phylogenetics right you must learn to use these applications. Early in this process, you will be doing yourself a favor if learn basic UNIX syntax and file architecture.