Figure 1.

Alignments as partitions of the set of sites. (Left) - Unaligned sequences: the class in red is ambiguous. It cannot take place into any alignment of the sequences. The green and orange classes are non-ambiguous. However, they are incompatible with each other. If the green class is accepted, then the orange one must be excluded. (Right) - An alignment of the sequences containing as equivalence class the green subset of sites. Each column of the complete alignment is a subset of sites. The corresponding partition is consistent: in particular, all the elements in a given column appear in the same order with respect to another column.