For the past few years, we’ve maintained a growing list of general advice for folks interested in doing applied phylogenetics. We’ve now transferred this page to the new site. The first piece of advice on this page is to use a simple text editor rather than a complicated word processor when working with input and output files from phylogenetic software; the figures below show how much of a difference this can make.
Fig 1: This is what a text file should look like when opened in a text editor (in this case, the text editor is TextWrangler).
Fig. 2: This is what the same text above looks like if we save it as a Microsoft .doc formatted file.
Drop us a line if you can think of other basic advice you’d like to see added to our list!
Figure 1: The impact of varying the shape parameter (alpha) on the gamma distribution.
Although the gamma distribution is widely used in phylogenetics, it remains somewhat of a mystery to many of the students in our annual workshop in applied phylogenetics. Acquiring a basic understanding of the gamma distribution is key to understanding how many widely-used phylogenetic methods work (e.g., MrBayes, BEAST, SIMMAP, BayesTraits). With a bit of help from Brian Moore, I’ve just posted a short tutorial that uses a series of simple R scripts and resulting figures to illustrate how and why the gamma distribution can assume such a wide range of shapes. I hope folks will find this tutorial useful, and encourage you to play around with the scripts I’ve posted to further your understanding of the gamma distribution. Drop me a line if you have any questions.