The phrase "alignment we test" is correct and usable in written English.
It can be used in contexts where you are discussing the evaluation or examination of alignment in a specific situation or framework.
Example: "In our research, we focus on the alignment we test to ensure that our findings are valid and reliable."
Alternatives: "alignment we evaluate" or "alignment we assess".
For the complete alignment we tested for appropriate models of nucleotide substitution using the Akaike Information Criterion (AIC) as implemented in Modeltest [ 42].
Since the cluster-specific residues between SAP30 and SAP30L in the sarcopterygian clusters were prominent in the alignment, we tested whether these residues are functionally relevant.
Using imputation quality thresholds from 0.3 to 0.9 as a requirement of inclusion during alignment, we tested the influence of stricter thresholds on imbalance precision and sensitivity using partial genotypes.
By analyzing the phylogenetic trees and sequence divergences of these two alternative alignments, we test the hypothesis that distantly related sequences with the same configuration of the inversion may cluster more closely than conspecific sequences with different forms of the inversion.
Since Bismark supports Bowtie2 only with the 'end-to-end' alignment model, we tested it in two modes: Bowite2-e2e and Bowtie.
For each alignment we used LRTs to test whether switches of selective pressure over time occurred (M2a vs M2a+S1 and M3 vs M3+S1), and for alignments with significant evidence for switches we also tested whether there was switching bias (M2a+S1 vs M2a+S2 and M3+S1 vs M3+S2).
Test data for alignment: We use the following three datasets to test the alignment accuracy of our method.
The quality of the alignment we have obtained can be tested by comparing the genomic positions of the aligned ORFs.
Following the M. musculus EST analysis, length filtering, and subsequent MUSCLE alignment, we obtained sequence alignments of 395 genes to test for evidence of positive selection.
To reduce the possibility that the initial EST test might have been affected by the alignment errors introduced by the methods in their mRNA alignments and repeated in the EST alignments, we repeated the test with an extra requirement that the set of introns must be the same in the mRNA alignments produced by every method.
