A Similarity Matrix is a type of graph comprised of multiple squares that create the matrix. These squares are aligned in a sequence. Scores with larger numbers are assigned to characters which are very similar. Characters that are dissimilar are assigned negative numbers. The overall goal of this matrix is to express similarity between two different data points which are being observed.
The Similarity Matrix that is displayed shows the similarity of phenotypes for 10 bacterial strains. There are nine different boxes, each with a different design. Each box represents the percentage of similarity between any two strands. As you can tell, the boxes that are completely black show those strands that are the same, or 100% alike.
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