When starting PermutMatrix, you are requested to choose the input file.
Its format should be the same as the one Eisen's Cluster expects or comply with the usual specifications described here.

Then a dialog window appears where you choose input data types, select hierarchical clustering methods or opt for the seriation process to be applied on the data.
The default options can be used.
Some options, like the nature of the data, cannot be modified afterwards.

The graphical data matrix appears as a colour matrix, with rows and columns in the same order as in the input file.

Then you can select the Display options which best display the data matrix.

The different data treatments are triggered via the Toolbar.

At any time, a pop-up menu is available with a right-click.

Some treatments can be applied to a sub-set of rows or columns.
To select a sub-set, select the chosen rows (columns) in the data matrix with the mouse; the selected rows (columns) are then displayed with a yellow frame.
When a tree is displayed, the set of rows (columns) borne by a branch can be selected by clicking on the branch.
Then the sub-tree is displayed in red, and the selected rows (columns) are displayed with a yellow frame.

The list of the identifiers of the selected elements can be displayed in a new window, via the pop-up menu.