There are few things that are more useful or necessary in evolutionary biology these days than learning new computational skills, including how to run software programs. For this, there are a variety of sources of information: journal articles (methods papers/sections), library books, online books (e-Books), workshops, online tutorials, and internet blogs like this one. Tutorials are among the best of these options given their practical focus, and because they often include step-by-step instructions with screenshots showing how to interact with GUIs, etc. However, not all tutorials are created equal, and many leave something to be desired.
I think that elsewhere on this site I’ve penned some pretty helpful posts on how to use BEAST software and related utilities. But when you see a really great tutorial, it makes you say, “Wow, this is really good, I wish I had written this.” That was my reaction when I recently saw a new (at least, new to me) BEAST2 tutorial written by the great Tracy Heath for the Bodega Bay Workshop in Applied Phylogenetics.
Here a link to Tracy’s tutorial:
Divergence Time Estimation using BEAST, by Tracy Heath
Bodega Bay workshop leaders have long posted their tutorials online, and theirs have also long been some of the best analysis tutorials available in our field; but this one may be the best Bodega tutorial that I’ve ever seen (there look to be some other new ones up from Bodega Bay though, so I’ll have to look at those before making a final call on that!). Why? Because it really seems that everything is accounted for. A PDF of detailed instructions with screenshots is given along with example input and output data plus a slideshow of the slides that Tracy actually uses to teach BEAST and guide users through its many possible options.
I think that everyone should go through this tutorial, regardless of how much experience you’ve had using BEAST. You might learn something you didn’t already know. This tutorial will also be a nice resource for those interested in writing labs for phylogenetics or molecular evolutionary analysis courses.
PS As the linked site and tutorial instructions emphasize, this tutorial is meant to be used with BEAST v2.1.3 or newer–if you disregard this point, all options in the tutorial may not be available to you.
~J