The phrase "alignment option" is correct and usable in written English.
It can be used in contexts where you are discussing choices or settings related to alignment, such as in design, formatting, or strategic planning.
Example: "In the software settings, you can choose the alignment option that best fits your layout preferences."
Alternatives: "alignment setting" or "alignment choice".
The separate alignment option aligns all sequences against different references separately in a run.
The iterative alignment option aligns sequences against the reference sequences in a pre-determined order.
Hexons genes from the HAdV-D genomes were aligned using ClustalW [50] alignment option available in the MEGA 4 program [51].
Sequences were organized into five separate data matrices using Mesquite 2.72 [ 34], and each aligned with the accurate alignment option (E-INS-i) in MAFFT 6.7 [ 35- 37] under default parameters.
The mtDNA sequences were aligned with the ClustalW multiple alignment option in BioEdit, version 4.8.10 [40].
Subsequently, these alignments were aligned using the profile-profile alignment option in MUSCLE.
The two groups of sequences were aligned using the ClustalW [50] alignment option available in the MEGA 4 program [51].
Open reading frames were translated into amino acid sequences and aligned by using the ClustalW alignment option in Geneious version 6.0.5 (www.geneious.com/).
The MAFFT FFT-NS-2 alignment option was used to align the 16S rRNA gene clone sequences of the IBS-D and healthy control (HC) libraries separately and together.
Sequences were multiply aligned using MAFFT39, considering the local alignment option with default settings for the other parameters, then optimized and phylogenetic trees were generated, using the FastTree methods40.
Following building the profile alignment for group I and group II separately, the two aligned profiles were merged using profile alignment option from ClustalX.
