This dialog box contains a set of analysis options for use in Maximum Parsimony analysis. Information from this dialog is used in the requested analysis, so it is important that you examine the options selected before pressing OK to proceed with an analysis.
Phylogeny Test and Options
To assess the reliability of the MP trees, MEGA provides the bootstrap test. You need to enter the number of replicates for this test if it is selected.
Tree Inference Options
Use this to select between the Subtree-Pruning-Regrafting (SPR), Tree-Bisection-Reconnection (TBR), Min-Mini, and Max-Mini Branch-and-Bound, heuristic search methods.
For the SPR and TBR methods, you may automatically obtain a set of initial trees by using the random addition option to produce the initial trees.
For all methods except for Max-Mini Branch-and-Bound, the MP search level can be set.
For the branch-and-bound search, an optimized Max-Mini Branch-and-Bound algorithm is used. While this algorithm is guaranteed to find all the MP trees, a branch-and-bound search often is too time-consuming for more than 15 sequences, although this number varies from data set to data set.
For all methods, you can set the maximum number of equally parsimonious trees to retain.
Substitution Model
Substitution Type
For protein-coding data, the analysis can be performed at the nucleotide or the amino acid level.
Genetic Code Table
If protein-coding data is to be analyzed at the amino-acid level, a genetic code for translating the data must be selected.
Data Subset to Use
This provides options for handling gaps and missing data in the analysis, specifying inclusion and exclusion of codon positions, and restricting the analysis to only some types of labeled sites (if applicable).
Gaps and Missing Data
You may choose to remove all sites containing alignment gaps and missing-information before the parsimony analysis begins using the Complete-deletion option. Alternatively, you may choose to retain all such sites. In this case, all missing-information and alignment gap sites are treated as missing data in the calculation of tree length. Your last option is Partial Deletion a.k.a. coverage where you may select a percentage where only sites above that percentage of unambiguity will be counted.
Select Codon Positions
You may select any combination of 1st, 2nd, 3rd, and non-coding positions for analysis. This option is available only if the nucleotide sequences contain protein-coding regions. If they do, you can choose between the analysis of nucleotide sequences or translated protein sequences. If you choose the latter, MEGA will translate all protein-coding regions into amino acid sequences and conduct the protein sequence parsimony analysis.
Labeled Sites
This option is available only if there are labels associated with some or all of the sites in the data. By clicking on the ellipses, you will have the option of including sites with selected labels. If you choose to include only labeled sites, then these sites will be the first extracted from the data and all other options mentioned above will be enforced. Note that labels associated with all three positions in the codon must be included for a full codon to be incorporated in the analysis.