The phrase "alignment of the underlying" is correct and usable in written English.
It can be used in contexts discussing the arrangement or coordination of foundational elements or principles in a system or framework.
Example: "The alignment of the underlying theories is crucial for the success of the project."
Alternatives: "coordination of the foundational" or "congruence of the basic".
However, the resolution power of the phylogenetic analysis in this case is low because the multiple alignment of the ATPases underlying the tree includes only 165 phylogenetically informative positions (see Additional files 3 and 4).
We found that the presence of these grooved topographical cues significantly enhanced VSMC aspect ratio, alignment, and oriented remodeling of the underlying extracellular matrix.
We also note that the performance of RAF on particular RNA families is often closely related to the accuracy of the underlying alignment and single-sequence models used to derive folding and alignment constraints.
We show that this instability is due to instabilities of the underlying alignment procedures that are, in turn, caused by sequence repeats.
In this study, only the safe branches of a tree topology will be considered when comparing trees resulting from distinct alignments, and we will confirm that, as expected, instabilities concerning these branches indicate instabilities of the underlying alignments.
Another advantage of storing the alignments without the underlying sequences is that it saves space, especially as reads become longer.
The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm.
In all these applications, the reliability and accuracy of the analyses depend critically on the quality of the underlying alignments.
In view of their rather restrictive definition, it was natural to guess that that instabilities of safe branches indicate instabilities of the underlying alignments.
