The phrase "alignments that cannot be" is correct and usable in written English.
It can be used in contexts discussing configurations, relationships, or agreements that are impossible or unachievable.
Example: "In this project, we need to identify alignments that cannot be established due to conflicting objectives."
Alternatives: "alignments that are impossible" or "alignments that cannot exist".
Moreover, the number of variable sites and particularly parsimony informative sites represent posthoc indices giving estimates of the amount of signal present in the alignments that cannot be justifiably projected to a different set of taxa or to a novel depth in a phylogeny, limiting their utility.
Alignments that cannot be divided are collected as isogroups, and branching structures between them are searched by traversal paths through connected branches, i.e. isotigs (isotigs and isogroups are Newbler-specific terms).
Short alignments (<15 bases) that cannot be visualized using Dotter are detected using the Zmap DNA Search pattern-matching tool (33).
More permissive alignment algorithms may also reduce the proportion of fragments that cannot be aligned, but could increase spurious alignments in complex genomes such as maize.
The proposed procedure guarantees a very good alignment between the lattice axes that cannot be directly translated to a good surface alignment.
All sequences in the General Training Set are formed by the training sequences that cannot be predicted by the sequence alignment method.
In this study, the SVM-LZ complexity pairwise algorithm is implemented on those test sequences that cannot be predicted by the sequence alignment method.
However, the number of alternative hypotheses that cannot be rejected increases for the sub-alignments containing the least conserved residues.
MapNext first conducts the unspliced alignment of all query reads, then conducts the spliced alignment of reads that cannot be aligned at the first stage.
Tophat takes the reads that cannot be directly mapped to the genome and breaks them into two parts for independent alignment.
