Analysis Preferences (Distance Computation)

In this dialog box you can select and view the desired options in the Options Summary.  Options are organized in logical sections. A yellow row indicates that you have a choice regarding the attribute in that row.  The three primary sets of options available in this dialog box are:

Analysis

Variance Estimation Method

Use this to specify whether to compute Distances only or Distances and Standard Errors using the selected estimation method.  If you select the latter, then you are given a choice as to how to compute it in the No. of Bootstrap Replications box.

When you compute average distance or diversity, only the bootstrap method is available for computing standard errors.

Substitution Model

In this set of options, you choose the various attributes of the substitution models.

Substitutions Type

Here you may select a substitutions type of Nucleotide, Syn-Nonsynonymous, or Amino Acid.  The selection in this row effects the available models in the model row.

Model

Here you select a stochastic modelHC_Models_for_estimating_distances for estimating evolutionary distance by clicking on the row then selecting a model for the current Substitutions Type. 

Substitutions to Include

Depending on the distance model or method selected, the evolutionary distance can be teased into two or more components.  By clicking on the row, you will be provided with a list of components relevant to the chosen model.

Transition/Transversion Ratio

This option will be visible if the chosen model requires you to provide a value for the Transition/Transversion ratio (R)RH_Transition_Transversion_Ratio_R.

Pattern among Lineages

This option becomes available if the selected model has formulas that allow the relaxation of the assumption of homogeneity of substitution patterns among lineages.

Rates among Sites

This option becomes available if the selected distance model has formulas that allow rate variation among sites.  If you choose gamma-distributed rates, then the 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 option becomes visible.

Data Subset to Use

These are options for handling gaps or 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 and Missing Data

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) as a percentage.

Codon A codon is triplet of nucleotides that codes for a specific amino acid. 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 the nucleotide sequences contain protein-coding regions and you have selected a nucleotide-by-nucleotide analysis.

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.

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 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.