The MSA overview will be showed automatically when you open an alignment. To show the simple MSA overview use the Show simple overview context menu item of the MSA overview.
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The following settings of the MSA overview are available:
Dispaly settings:
Graph type - sets the graph type: histogram, line graph or area graph.
Orientation - sets the orientation: top to buttom or buttom to top.
Set color - sets the gpaph color.
Calculation method - sets the calculation method: strict, gaps, clustal or highlighting.
To use these settings go to the corresponding context menu items of the MSA overview.