The phrase "a third alignment" is correct and usable in written English.
It can be used when referring to a third instance or version of an alignment in various contexts, such as in discussions about strategies, plans, or configurations.
Example: "After reviewing the first two alignments, we decided to implement a third alignment to better meet our objectives."
Alternatives: "a tertiary alignment" or "the third configuration".
A second alignment was performed to remove poorly aligned regions in the dataset using Gblocks 0.91b [ 103] under a relaxed approach.
For handling inverted transitions we use a second alignment table, X G ′ for aligning T with G′, which is initialized in a similar fashion to X G (naturally S m values are obtained for the complementary nucleotide).
In this case, acquire a relatively quick undistorted anatomical scan (e.g., T1 or fast-spin-echo T2) using a matched set of slices, then use this anatomical volume for a first alignment step.
E.g., perform an initial alignment in a rodent using an anatomical scan, and then perform a second alignment step on distorted EPI data (with matching slices) by starting with the first parameter set but eliminating the slice position (z) and scaling (size-z) from the parameter set, because the slice-selection step is the same for anatomical and EPI data.
A second alignment that maximized the number of sequences by allowing some sequences to be missing was also constructed.
This alignment was then fitted to a second alignment based on a needle alignment of E. coli Slt70 and the RvhB1 protein from Brucella suis [116].
However the time necessary for the two DNA molecules to reach a first alignment is not the only relevant parameter for efficient repair.
For a second alignment, comprising bat orthologues, the MAPP score of each amino acid variant was derived, together with the score of all other variants at the same site in the alignment that differed from the ancestral sequence by an equal or fewer number of nucleotide substitutions.
A first alignment was performed using the Muscle program [ 39].
