The phrase "after the alignment was" is correct and usable in written English.
It can be used in contexts discussing processes, adjustments, or changes that occur following an alignment, such as in technical, scientific, or organizational settings.
Example: "After the alignment was completed, we observed significant improvements in performance metrics."
Alternatives: "following the alignment" or "subsequent to the alignment".
For the construction of the phylogenetic trees of the GH families the sequences of the family members were aligned using Muscle (version 3.8.31) [ 58] after which the alignment was used to generate a bootstrapped minimal evolution tree (1000 bootstraps) using MEGA4 [ 59].
After concatenation, the alignment was trimmed using trimAl [ 77].
On the other hand, after 1984, codon 137 of the alignment was identified as positively selected considering all the data after 1984 and in 9 out of 10 random data sets analysed.
If the alignment score exceeds the user-defined threshold, the aligned region plus the remainder after the alignment are removed.
After the alignment is manually adjusted on the basis of this observation, models B and C show better fits for fragments 45 49, 143 149, and 169 172, as these regions are predicted to be helices in helix bundles.
COMPASS [ 41] is a Perl script that uses Lastz [ 58] to align assembly scaffolds to a reference, after which the alignment is parsed (using SAMTools [ 75]) to calculate alignment and coverage island lengths (see Figure 7), which are used to create cumulative length plots (e.g., Figure 10), as well as to calculate coverage, validity, multiplicity, and parsimony metrics.
b The length of analyzed data, after the ambiguous areas of the alignment were removed by Gblocks 0.91b.
c The length of all introns concatenated, after the ambiguous areas of the alignment were removed by Gblocks 0.91b with no gap (Com1), half gap (Com2), and all gap (Com3) parameters.
The alignment is converged after 3-4 iterations.
The filtering is implemented as a second MapReduce algorithm run immediately after the alignments are complete.
