Analysis Preferences (Maximum Likelihood)

Analysis Preferences (ML)

In this dialog box, you can view and select desired settings for Maximum Likelihood tree search. Available options are organized into logical sections. Analysis options which have multiple settings available are displayed in white boxes. To view the available settings for an option, click on its box. The primary categories of options available for ML analysis are:

Phylogeny Test

To assess the reliability of a phylogenetic tree, MEGA provides two methods:

 Felsenstein's Bootstrap testHC_Bootstrap_Test_Phylogeny. The full data is randomly sampled (with replacement ) for a desired number of replicates.

The Adaptive approach that will automatically determine the number of bootstrap replicates to perform. When selected, you can set the threshold (default is 5.0) to be used when determining the number of replicates to perform. When using this option, MEGA will initially perform 25 replicates. MEGA will then add replicates one-by-one until all bootstrap values have a standard error that is <= the specified threshold. If the stopping condition is not met, MEGA will stop adding replicates once 500 have been completed.

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 EditorHC_Code_table_editor from within this option.

Model/Method

Here you can select a stochastic modelHC_Models_for_estimating_distances  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 According to the gamma distribution, the substitution rate often varies from site to site within a sequence. The shape of this distribution is determined by a value known as the gamma parameter, which is also known as the shape parameter.RH_Gamma_parameter).

Data Subset to Use

These are options for handling gaps and missing data, including or excluding codon A codon is triplet of nucleotides that codes for a specific amino acid. positions, and restricting the analysis to labeled sites Sites in a sequence alignment can be categorized and labeled with user-defined symbols. Each category is represented by a letter or a number. Each site can be assigned to only one category, although any combination of categories can be selected for analysis. Labeled sites work independently of and in addition to genes and domains, thus allowing complex subsets of sites to be defined easily., if applicable.

Gaps/Missing Data Treatment

For this analysis setting, you may choose to remove all sites containing alignment gaps Phylogenetic analysis on two or more DNA or amino acid sequences requires that the sequences be aligned so that the substitutions can be accurately enumerated. During alignment, gaps must be introduced in sequences that have undergone deletions or insertions. These gaps are known as alignment gaps or indels. and missing information before the calculation begins (Complete-deletionRH_Complete_Deletion_Option option). Alternatively, you may choose to retain all such sites initially, excluding them as necessary in the pairwise distance estimation (Pairwise-deletionRH_Pairwise_deletion_option option), or you may use Partial-DeletionRH_Partial_Deletion_Option (Site Coverage Cutoff ) as a percentage.

Codon Positions

Check or uncheck the boxes for any combination of 1^st, 2^nd, 3^rd, 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 labelsRH_Labeled_Sites. 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 Sites in a sequence alignment can be categorized and labeled with user-defined symbols. Each category is represented by a letter or a number. Each site can be assigned to only one category, although any combination of categories can be selected for analysis. Labeled sites work independently of and in addition to genes and domains, thus allowing complex subsets of sites to be defined easily., 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 A codon is triplet of nucleotides that codes for a specific amino acid. must be included for a full codon A codon is triplet of nucleotides that codes for a specific amino acid. to be incorporated in the analysis.

Tree Inference Options

ML Heuristic Method

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

System Resource Usage

Number of Threads

Specify the maximum number of threads that MEGA will use for the heuristic search and branch length estimation. In testing, the greatest reductions in computational time were achieved when using between 3 and 5 threads. Using more than 5 threads can further reduce computational time required but with quickly diminishing improvements.