Phylogeny | Construct Phylogeny | Maximum Parsimony…
This command is used to construct phylogenetic trees under the maximum parsimony criterion. For a given topology, the sum of the minimum possible substitutions over all sites is known as the Tree Length. The topology with the minimum tree length is known as the Maximum Parsimony tree.
The phylogenetic tree(s) inferred using this criterion are unrooted trees, even though, for ease of inspection, they are often displayed in a manner similar to rooted trees.
MEGA includes the Max-mini branch-and-bound search, which is guaranteed to find all the MP trees. However, it is often too time consuming for more than 15 sequences. In those cases, you should use the Close-Neighbor-Interchange (CNI) algorithm to find the MP tree. CNI is a branch swapping method that begins with a given initial tree. You can ask MEGA to automatically obtain a set of initial trees by using the Min-mini algorithm with a given search factor. Alternatively, you can produce the initial trees by providing your own topology or by using the random addition option. These options are available in the MP Tree Tab of the Options dialog box and are displayed before the phylogenetic analysis begins. Note that these CNI branch-swapping procedures may not produce the best MP trees or all the MP trees.
By default, all nucleotide (or amino acid) changes are weighted equally in MEGA (standard parsimony). However, for nucleotide sequences, you have the option of conducting a transversion parsimony analysis in which only transversional changes are considered for calculating the tree length. In addition, through the Analysis Preferences/Options dialog box, you are given options on which subset of sites to include, and whether to conduct a test of the inferred tree.