7.6.1. Using MEGA

The program MEGA (Molecular Evolutionary Genetics Analysis; http://megasoftware.net) (Tamura et al., 2011), currently available as version 5.05, is continually being updated and improved. Note: use of MEGA will require the user to download and install the freely available software to their computer. MEGA 5 can be used as a platform to complete all of the above steps (building your sequence data file, alignment using Clustal or MUSCLE, and trimming sequence data). It gives the user the ability to construct phylogenies using distance based (i.e. Neighbour Joining) and character based (i.e. Maximum Likelihood) methods (see Table 1) and test them using bootstrapping. It also includes a tree viewer that allows for some editing of the final output tree and many additional features not covered here. Constructing and testing phylogenetic trees