Читать книгу Principles of Microbial Diversity - James W. Brown - Страница 56

The similarity matrix is just a table of fractional similarities, for example, in this alignment of six sequences with 20 positions.

Just count the fraction of identical bases in every pair of sequences in the alignment.

The similarity values for all pairs of sequences are calculated in the same way and assembled into a table:

In this example, sequences A and B are 0.90 (90%) similar, A and C are 0.75 similar, B and C are 0.75 similar, and so forth. Note that values on the diagonal (A:A, B:B, …) do not need to be calculated; they are always 1. Likewise, there is no reason to calculate both above and below the diagonal; the value for X:Y is the same as that for Y:X, so the second calculation would be redundant.