Before an analysis run can be started, you must choose which sequences should be used for it, as not all analysis methods will work on any number of sequences, and some methods are better suited to large numbers of sequences than others.
By default, all sequences within an alignment are selected when a new TOPALi project file is created. Each selected sequence is shown (highlighted) in the list that forms the left-hand side of the Sequences display pane.
Manually selecting sequences
To manually select sequences, simply click them with the mouse. Ctrl-click to select multiple individual sequences, or Shift-click to select consecutive blocks of sequences.
Automatically selecting sequences
To select all sequences in an alignment, select Alignment | Select Sequences | All from the menu bar or press Ctrl-A.
To deselect all selected sequences, select Alignment | Select Sequences | None from the menu bar.
To only select sequences that are unique, select Alignment | Select Sequences | Unique Only from the menu bar. This option will select all sequences that are truly unique, along with the first sequence from each group of duplicate sequences that may exist.
To invert the currently selected sequences, select Alignment | Select Sequences | Invert Selection from the menu bar.