Читать книгу Principles of Microbial Diversity - James W. Brown - Страница 54

In chapter 3, we covered the first three steps of a phylogenetic analysis, leaving the final step toward which the others build. The steps in a phylogenetic analysis are as follows:

1 1. Decide which gene and species to analyze (small-subunit ribosomal RNA [SSU rRNA])

2 2. Determine the gene sequences (polymerase chain reaction [PCR] and DNA sequencing, database “mining”)

3 3. Identify homologous residues (sequence alignment)

4 4. Perform the phylogenetic analysis

The most common type of phylogenetic analysis is tree construction. A tree is nothing more than a graph representing the similarity relationships between the sequences in an alignment. This is why we’ll be going through this process in such detail, to show that tree construction is not rocket science but involves straightforward mathematical transformations of sequence data.

There are several methods for building trees. In this chapter, we cover the neighbor-joining method in some detail as an example, because it is conceptually straightforward and commonly used. In the next chapter, we briefly cover some other approaches.