Analysis Preferences (Fisher's Exact Test)

When the numbers of codons or the total numbers of synonymous and/or nonsynonymous substitutions are small, the large sample Z-testHC_Test_of_Selection_Tab is too liberal in rejecting the null hypothesis.  In these cases, tests of selection can be conducted to examine the null hypothesis of the neutral evolution.  Only the Nei-Gojobori and Modified Nei-Gojobori methods can be used for this test because it requires the direct computation of the numbers of synonymous and nonsynonymous differences, and the number of synonymous and nonsynonymous sites.  It should be used only when sequences show a small number of differences. To conduct Fisher’s Exact Test, you need to specify two specific options:

Substitution Model

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

Substitutions Type

Here you are limited to Syn-Nonsyn.

Model

By clicking on the row currently selected model, you may select a stochastic modelHC_Models_for_estimating_distances for estimating evolutionary distance.  This will reveal a menuHC_Models_for_estimating_distances containing two different options: the originalNei_and_Gojobori_1986 or modifiedZhang_et_al_1998 Nei & Gojobori methods.

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.

Data Subset to Use

These options handle gaps and missing data and restrict 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.

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 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.