The phrase "alignment was assessed using" is correct and usable in written English.
It can be used in contexts where you are describing a method or approach for evaluating or measuring alignment in a study or analysis.
Example: "In our research, alignment was assessed using a series of statistical tests to ensure accuracy."
Alternatives: "alignment was evaluated with" or "alignment was measured by".
Alignment was assessed using an image intensifier, and the appropriate size of the opening wedge was determined on the basis of the preoperatively planned correction.
All final alignments had a norMD score > 0.6 and have been provided in Additional file 7. The most appropriate protein evolutionary model for each alignment was assessed using ModelGenerator v.85 [ 83].
The software output includes summary statistics of probe set intensity such as signal and p-values for detection (detection p-values) testing whether or not signal was significantly greater than 0. Quality of the automated grid alignment was assessed using a MATLAB (The MathWorks, Natick, MA) script [ 11].
Additionally, the knee joint alignment was assessed using Fraser et al.'s criteria [ 12] and classified into three: excellent (TFA valgus 5 9° in female, valgus 4 7° in male), good (within 4° from the normal range), or poor (out of 4° from the normal range).
These proteins were aligned using T-Coffee (Notredame et al. 2000) and the alignment quality was assessed using Transitive Consistence Score (TCS, Chang et al. 2015).
Multiple alignment quality was assessed using Guidance (Penn et al. 2010).
Multiple sequence alignment quality was assessed using the HoT-method (Landan and Graur 2007).
Alignment quality was assessed using average parsimony score (Fitch 1971) in sliding window analysis, where we compared the average score of the alignment obtained with the average score of a randomized alignment with gap retention.
The conservation of codons was assessed using alignments containing S. purpuratus, A. fragilis, and S. franciscanus.
Nucleotide variability of collembolan mtDNA (see Additional file 1: dist.jpg) was assessed using thirteen alignments of the PCGs.
The presence, in the 13 genome sequences analyzed, of 78 putative virulence-associated genes previously reported by Camejo et al. [ 45] was assessed using whole genome alignments produced with Mauve 2.3.0.
