Analysis Preferences (Maximum Likelihood)

Analysis Preferences (ML)

In this dialog box, you can view and select desired settings for options which are listed in the Options Summary tab. Available options are organized into logical sections. A yellow row indicates an analysis option for which there are multiple settings available. To view the available settings for an option, click on its row. The five primary categories of options available for ML analysis are:

Phylogeny Test

To assess the reliability of a phylogenetic tree, MEGA provides the Bootstrap test. When selected, this test requires you to enter the desired number of replicates.

Substitution Model

In this set of options, you can select various attributes of the substitution models for DNA and protein sequences.

Substitutions Type

Here you may select a substitution type of either Nucleotide or Amino Acid, depending on the active sequence data. The selection in this row determines the models of evolution that will be available in the Model/Method row.

Genetic Code Table (displayed for protein coding nucleotide data only)

By accessing this option, you can select from a list of genetic code tables for automatically translating codons into amino acids. Alternatively, you can open a Code Table Editor from within this option.


Here you can select a stochastic model for estimating evolutionary distance by clicking on the row then selecting from one of the models that are applicable for the currently selected Substitutions Type.

Rates and Patterns

Rates among Sites

This option will be enabled if the selected model has formulas that allow rate variation among sites. If you choose gamma-distributed rates, then the No of Discrete Gamma Categories option becomes visible (see Gamma parameter).

Data Subset to Use

These are options for handling gaps and missing data, including or excluding codon positions, and restricting the analysis to labeled sites, if applicable.

Gaps/Missing Data Treatment

For this analysis setting, you may choose to remove all sites containing alignment gaps and missing information before the calculation begins (Complete-deletion option). Alternatively, you may choose to retain all such sites initially, excluding them as necessary in the pairwise distance estimation (Pairwise-deletion option), or you may use Partial-Deletion (Site Coverage Cutoff ) as a percentage.

Codon Positions

Check or uncheck the boxes for any combination of 1st, 2nd, 3rd, and non-coding positions for analysis. This option is available only if you are analyzing nucleotide sequences which contain protein-coding regions and you have selected a nucleotide-by-nucleotide analysis.

Labeled Sites

This option is available only if some or all of the sites have associated labels. By clicking on the row, you will be provided with 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. Then 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.

Tree Inference Options

ML Heuristic Method

This option allows you to specify either the Nearest-Neighbor-Interchange (NNI) or Subtree-Pruning-Regrafting (SPR) tree searching strategy.