Fig. 5
From: HH-suite3 for fast remote homology detection and deep protein annotation
Predecessor pair states for backtracing the Viterbi alignments are stored in a single byte of the backtrace matrix in HH-suite3 to reduce memory requirements. The bits 0 to 2 (blue) are used to store the predecessor state to the MM state, bits 3 to 6 store the predecessor of GD, IM, DG and MI pair states. The last bit denotes cells that are not allowed to be part of the suboptimal alignment because they are near to a cell that was part of a better-scoring alignment