Performing the calculations

Performing the calculations and sorting as well as opening the dialog of principal components' plots can be completed with use of the "Calculate" commands' group of the main menu:

• Consensus - to calculate the consensus for the set of sequences that are in the display area.
• Conservation - to calculate the conservatism of sequences. The conservatism is calculated in groups.
• Remove redundancy - to remove the sequences with similarities to the consensus below the defined threshold value. On executing this command the "Enter redundancy…" dialog with "Percent identity" entry field, where the appropriate value should be defined, appears. After completing the entry press the "OK" button.
• Sort - sequences' sorting modes:
  • Sort by pairwise identity - to sort by identity in pairs
  • Sort by ID - to sort in alphabetical order
  • Sort by group ID - to sort by groups first and then by alphabetical order in groups.
  • Sort by tree - to sort sequences by their order in a tree.
• Principal Component Analysis - to perform the calculating and visualizing the principal components (see Principal components).
• Calculate all - to calculate the consensus, the conservatism and the principal components.
• Auto calculate - to recalculate the consensus, the conservatism and the principal components after each removal of lines or columns.