Bifurcation rules allow a subsequence-pair (Xij, Ykl) to be composed from two adjoining subsequence-pairs (Xim, Ykn) and (Xnj, Yni). For this to be permitted by the constraints, the X-fold envelope (upper triangular grid) must contain subsequences (i, m), (m, j) and (i, j) (black dots), the Y-fold envelope (rightmost triangular grid) must contain subsequences (k, n), (n, l) and (k, l) (black dots) and the alignment envelope (rectangular grid) must contain cutpoints (i, k), (m, n) and (j, l) (short diagonal lines). The filled cells in the rectangular grid show the nucleotide homologies highlighted in the alignment. Note that all co-ordinates (i, j, k, l, m, n) lie on the grid-lines between nucleotides.
Holmes BMC Bioinformatics 2005 6:73 doi:10.1186/1471-2105-6-73