Читать книгу Principles of Microbial Diversity - James W. Brown - Страница 73

The process of generating phylogenetic trees as described in chapter 4 is straightforward. This is a gross simplification. Phylogenetic analysis is an entire scientific area of study, and the material that has been presented is very highly simplified. In this chapter we touch (just touch) on some of the complexities.

However, before thinking about more refined substitution models, treeing algorithms, or alternative sequences, keep one thing in mind: the most important thing by far that is needed to get a good, robust tree is to start with a good alignment. The simple and fast neighbor-joining method, using the Jukes and Cantor substitution model, usually gives perfectly usable trees if given a good small-subunit ribosomal RNA alignment to work with. Combined with bootstrapping (see below), this method is probably used more than any other for the creation of published trees.