The sequences are displayed in different Views, of which any number can be opened. Currently two types are available: In the Alignment View the sequences are shown as strings, in the Schematic View schematically as recangles.
Using the mouse cursor any sequences or parts of them can be selected and then analyzed by one of the Explorer algorithms, e.g. by the MACAW algorithm, which identifies regions of high similarity.
A block is a set of subsequences of equal length. The Explorer algorithms yield as result a list of blocks, which can then be edited. Those which are deemed to be important can be marked, i.e. saved, and highlighted in the alignment. Marked blocks can be aligned (linked), which happens automatically by inserting gaps ('-') into the alignment.
By the block editor any Explorer result or existing block can be viewed and modified. The quality of a block can be assessed by means of scores and a significance value.