All the above FMD algorithms try to speed up the full mode decision process from different aspects.
Electromagnetic field calculations of the non-axisymmetric cavities carried out by using MAFIA 3D code (Weiland, 1986) gave the RF wall losses and the full mode spectrum.
This heuristic is called the coarse mode (and the original approach is called the full mode).
This suggests the current practical range of the full mode of the SIT bound.
Also, the RAM usage is significantly lower than the full mode (up to 50% lower in our experiments).
When the number of taxa increases, the coarse mode is likely to run faster than the full mode, but the difference is less significant.
In the full mode, once the index containing target-specific k-mers has been created, CLARK creates a "dictionary" that associates k-mers to targets.
For five larger datasets, there are a small number of test cases that are too slow to run the full mode, and are excluded.
Some numerical examples are given to show the effectiveness of the full-mode approach by comparing the results with those from the two-mode and multi-mode procedures.
The proposed method avoids the exhaustive full mode search method, which includes all seven modes plus two intra modes for RDO calculation.
