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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; ω1 = (0,0,0,0)T, ω2 = (0,1,0,1)T, ω3 = (1,1,0,1)T, ω4 = (0,0,1,1)T, ω5 = (0,,1,1)T, andω6 = (0,,0,1)T. This portion of the alignment, therefore, contains 2 copies of ω1, 2 copies of ω2, 3 copies of ω3, and one copy each from ω4, ω5, and ω6.