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From:
Published online 2010 May 6. doi: 10.1155/2010/167408

Figure 1

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A fragment of a hypothetical input for a 4-species analysis. This is a segment of a multiple alignment of 4 orthologous genes. Notice the gap in one of the genes, designated by * for unknown character. Among the 10 sites in this alignment fragment, there are 6 unique patterns; ω 1 = (0,0,0,0)T, ω 2 = (0,1,0,1)T, ω 3 = (1,1,0,1)T, ω 4 = (0,0,1,1)T, ω 5 = (0,*,1,1)T, and  ω 6 = (0,*,0,1)T. This portion of the alignment, therefore, contains 2 copies of ω 1, 2 copies of ω 2, 3 copies of ω 3, and one copy each from ω 4, ω 5, and ω 6.

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