The phrase "alignment was removed" is correct and usable in written English.
It can be used in contexts where a specific alignment, such as text or object positioning, has been taken away or eliminated.
Example: "After reviewing the document, I noticed that the alignment was removed, making it difficult to read."
Alternatives: "alignment has been eliminated" or "alignment has been deleted."
Poorly aligned regions from this alignment were removed with the Gblocks 0.91b program [ 74], using the default settings, except that allowable gap position was selected to half.
The ambiguously aligned regions in each alignment were removed and optimized using GBLOCKS 0.91b [ 89] with the -b2 option (minimal number of sequences for a flank position) set to 13.
Non-unambiguously aligned regions in the alignment were removed based on BLOSUM62 (Henikoff S and Henikoff JG 1992) scoring matrix values allowing each aligned amino acid position with 10% of divergence, and converted to Phylip format.
New gaps which were introduced in the aligned template sequence during pairwise alignment are removed, and to maintain the alignment, the nearest gap character in the aligned candidate sequence is also removed.
Sequences were aligned [ 36] and regions of ambiguous alignment were removed when necessary.
If the alignment score exceeds the user-defined threshold, the aligned region plus the remainder after the alignment are removed.
The poorly aligned and divergent regions in each codon alignment were removed using GBLOCKS 0.91b (Castresana 2000) and the option – t = c for exclusion of complete codons.
Second, poorly aligned positions and divergent regions in each KOG alignment were removed by using Gblocks 0.91b [ 27].
As 10 out of 20 Acari species in our dataset are ticks all positions aligning to AGG codons in the final amino acid alignment were removed.
Gaps, poorly aligned and highly divergent regions of the resulting multiple sequence alignment were removed using Gblocks [32].
