The phrase "alignment data set" is correct and usable in written English.
It can be used in contexts related to data analysis, machine learning, or research where data is organized to ensure consistency or accuracy in results.
Example: "The researchers compiled an alignment data set to improve the accuracy of their predictive models."
Alternatives: "calibration data set" or "reference data set".
In total, the full alignment data set was compared to nine different topologies.
This integrated alignment data set was used to edit the physical map.
Each alignment data set was then filtered for pairs of reads with only one unambiguous alignment and convergent orientation (inward-facing read pairs).
To investigate the possibility of tRNA posttranscriptional modifications, we used the non-stringent small RNA alignment data set (defined above) and used WebLogo to characterize nucleotide mismatches [ 60].
The analysis of 100 bootstrap resamples of the alignment data sets was performed using PHYLIP.
RNAaliduplex is designed to facility the search for conserved RNA-RNA interaction sites in large alignment data sets.
For both the LSUrRNA and SSUrRNA sequence alignment data sets, we used a neighborhood of 50 nt (and 100 nt) in fitting the loess curve.
For each of the eutherian mammal alignment data sets, phylogenetic trees were constructed using raxml version 7.0.4 (Stamatakis 2006; Stamatakis et al. 2008).
Third, we conducted a principal components analysis of the amino acid frequency matrix at all sites of the 21 protein alignment data sets and obtained four major classes (or profiles) of amino acid frequency distribution at sites.
In general, we have observed that various methods gave expected results (confidence sets larger for WLS than for GLS, and closer to SH set size) when there was a large number of site patterns in the alignment (data sets 1, 6, 9 and 12), even when the percent of unresolved quartets was quite high (data set 1).
Although the long-branch taxa were removed, the ML trees inferred from the four different reduced alignment data sets showed that the pycnogonids are consistently clustered with the terrestrial spider H. langzhouensis [See additional file 5A, C, D], except for the ML tree with the 21 taxa in which A. bituberculata appears as a sister group of euchelicerates [See Additional file 5B].
