The phrase "alignment were identified" is not correct in written English.
It should be "alignments were identified" or "alignment was identified" depending on the intended meaning.
Example: "In the study, several alignments were identified that contributed to the overall success of the project."
Alternatives: "alignments were detected" or "alignment was found".
Poorly aligned and gap-rich regions of the alignment were identified by eye and excluded from the analyses.
Ambiguously aligned hypervariable loop regions within the 870 taxa alignment were identified by eye and coded as binary absence (gap) and present (any base) data [ 64] before fed into RAxML version 7.2.2 [ 65].
Ambiguous regions in the resulting alignment were identified and removed using GBlocks 0.91b [92].
Reads that mapped to the genome through a gapped alignment were identified and isolated.
Phylogenetic informative SNP sites (i.e., SNPs shared by two or more strains in the alignment) were identified by two different methods.
Multiple layers of fibers of differing fiber density and alignment were identified in a number of samples, whereas other capsules were composed of a single-collagen layer of variable density.
[25] reported that open wedge osteotomy should be the first stage of treatment in patients with chronic isolated PLC injuries if genu varus alignment is identified.
Interestingly, the structural alignment is identified for each cutoff value, and our approach appears to be robust regarding this parameter (data not shown).
The structural alignment is identified correctly using the ANOLEA/All, the ANOLEA/ROI or the ANOLEA/SSE predictors (Fig. 8A, 8B and 8C, respectively).
While the best alignment scores were generally reached before the tenth step in each SATé run, the overall best scored alignment was identified only after many more iterations on a 8-core cluster (Table S2).
Exons too short to be identified by read alignment are identified by Tophat junction alignments.
