Chapter 2 An Introduction to Phylogenetics and the Tree of Life

We present an introduction to experimental design and hypothesis testing in phylogenetics, guiding the reader through the series of steps that are generally involved in making phylogenetic trees. These include choosing a phylogenetic question, selecting the appropriate sequences to analyse, aligning sequences and assessing the quality of sequence alignments, choosing the appropriate phylogenetic methods and interpreting the results. We provide a brief introduction to the freely available, open source software and Web services that can be used to perform these tasks and discuss the difficulties most frequently encountered when building phylogenies, along with some possible solutions. To provide biological context, we will frame our discussion in terms of a very interesting (and still controversial) problem: the reconstruction of the tree of life from ribosomal RNA sequences.

Source: Methods in Microbiology - December 4, 2014 Category: Microbiology Source Type: research