Sequence Data Subset Selection

Any subset of sequence data can be selected for analysis using the options in the Data menuHC_Data_Menu_in_sequence_Data_Explorer.  You may:

Select Taxa A taxon is the individual unit whose evolutionary relationship is being investigated. Depending on the study, “taxa” may refer to species, populations, individuals, or sequences within an individual.RH_Taxa (sequences) or GroupsRH_Groups_of_taxa of taxa A taxon is the individual unit whose evolutionary relationship is being investigated. Depending on the study, “taxa” may refer to species, populations, individuals, or sequences within an individual. through the Setup/Select Taxa A taxon is the individual unit whose evolutionary relationship is being investigated. Depending on the study, “taxa” may refer to species, populations, individuals, or sequences within an individual. & GroupsHC_Setup_Taxa_Groups_Dlg dialog box,

Choose Domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog.RH_Domains and GenesRH_Gene through the Setup/Select Genes & Domains A domain is a continuous block of sites in a sequence alignment. A domain can be free-standing or assigned to genes and protein-coding (e.g., exons) or non-coding (e.g., introns). Domains can be defined in the input data, and can be defined and edited in the Setup Genes Domains dialog.HC_Genes_Domains_Dialog dialog box,

Items 1 and 2 lead to the construction of a primary data subset, which is maintained until it is modified in the two dialog boxes mentioned in the above items or in the Sequence Data ExplorerHC_Sequence_Data_Explorer.

Select any combination of Codon A codon is triplet of nucleotides that codes for a specific amino acid.RH_Codon Positions to use through the Analysis Preferences/Options dialog box from the Data | Select PreferencesHC_Select_Preferences menu item in the main interface. 

Choose to include only the 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.RH_Labeled_Sites through the Data | Select PreferencesHC_Select_Preferences menu item.

Decide to enforce Complete-DeletionRH_Complete_Deletion_Option or Pairwise-DeletionRH_Pairwise_deletion_option of the missing data and 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.RH_Alignment_Gaps.

Items 3, 4, and 5 provide the second level of data subset options.  You are given relevant choices immediately prior to the start of the analysis.  Therefore, these choices are secondary in nature and are specific to the currently requested analysis.  The Analysis Preferences dialog box remembers them for your convenience and provides them as a default the next time you conduct an analysis that utilizes those options.