Therefore, F and S sites along the alignment are expected to be segregated into a small number of groups.
Considering Kimura's neutral theory of molecular evolution, it is logical to apply a stochastic model at the level of DNA substitutions to construct probabilistic description of what molecular alignments are expected to be observed, given a proposed evolutionary history (tree topology and edge lengths).
However, the alignment accuracy of these particles is expected to be limited by weaker contrast (Henderson, 1995), and we expect improvements similar to those seen in our simulation when using exposures that significantly exceed the optimal exposure and applying the exposure filter described here.
However, as read lengths increase and alignment algorithms are further developed this is expected to be feasible in the near or intermediate future.
However, it brings serious range migration, which is expected to be corrected in the conventional range alignment step.
Because DIALIGN does not perform alignments following a guide tree, the alignments produced were expected to be relatively robust to artifacts that may be introduced when aligning divergent sequences in a pairwise manner [ 57].
None of these alignments can be expected to be error-free, but the fact that there are so many between the same two groups, and that sequence and functional relationships have been established for decades[20] implies that the existence of the edges if not the details of the alignment underlying each individual edge is reliable.
The quality of the alignment can therefore be expected to be higher than normal when medical terminology systems are used as sources.
The latter is challenging because, in the SAM format, an alignment of a read pair is described by a pair of alignment records, which cannot be expected to be adjacent to each other.
Most comparative motif discovery approaches rely in some way on multiple sequence alignments, in which regulatory signals are expected to be well-aligned.
