Today most phylogenetic trees are built from molecular data: DNA or protein sequences. MEGA is available for use on PCs and Macs from ProtocolĪ phylogenetic tree is an estimate of the relationships among taxa (or sequences) and their hypothetical common ancestors ( Nei and Kumar 2000 Felsenstein 2004 Hall 2011). Here a step-by-step protocol is presented in sufficient detail to allow a novice to start with a sequence of interest and to build a publication-quality tree illustrating the evolution of an appropriate set of homologs of that sequence. Finally, MEGA provides a powerful and flexible interface for the final step, actually drawing the tree for publication. Here we illustrate the maximum likelihood method, beginning with MEGA's Models feature, which permits selecting the most suitable substitution model. For the third step, construction of a phylogenetic tree from the aligned sequences, MEGA offers many different methods. For the second step, alignment of those sequences, MEGA offers two different algorithms: ClustalW and MUSCLE. The first step, identification of a set of homologous sequences and downloading those sequences, is implemented by MEGA's own browser built on top of the Google Chrome toolkit. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. In the example illustrated here, the program MEGA is used to implement all those steps, thereby eliminating the need to learn several programs, and to deal with multiple file formats from one step to another (Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.
This Protocol describes the several steps required to produce a phylogenetic tree from molecular data for novices. In fact, it is a fairly straightforward process that can be learned quickly and applied effectively. Phylogenetic analysis is sometimes regarded as being an intimidating, complex process that requires expertise and years of experience.
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