Phylogeny | Construct/Test Minimum Evolution Tree
This command is used to construct a phylogenetic tree under the minimum evolution criterion. In this method the sum, S, of all branch length estimates, i.e.
S = bi,
is computed for all plausible topologies, and the topology that has the smallest S value is chosen as the best tree: the ME tree. This criterion does not require the assumption of evolutionary rate constancy as needed in the UPGMA analysis. Therefore the inferred phylogenetic tree is an unrooted tree, even though, for ease of inspection, it is often displayed in a manner similar to rooted trees.
MEGA employs the Close-Neighbor-Interchange (CNI) algorithm to find the ME tree. This is a branch swapping method, which begins with a given initial tree. You can ask MEGA to automatically construct a Neighbor-Joining (NJ) tree and use that as the starting tree. Alternatively, you can provide your own topology. Note that the final tree produced after this search is not guaranteed to be the ME tree. These options are available in the Analysis Preferences dialog box, which is displayed before the phylogenetic analysis begins. This dialog box also allows you to specify the distance estimation method, subset of sites to include, and whether to conduct a test of the inferred tree.