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The testing of our covariation detection method on 15 other alignments showed that the accuracy of contact prediction is highly variable depending on which sequence alignment is used, and useful levels of prediction accuracy were obtained with only approximately one-third of alignments.
In comparison, the nearest genetic distance method determines the identity of a sample based on which sequence in the database has the smallest genetic distance from the query sequence; this distance must be less than a distance threshold.
Additionally, BLAST E-values and scores are not symmetric for a given comparison between two sequences, the alignment, score, and E-value can vary depending on which sequence is used as the query.
Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
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Comparing human DNA with that of close and distant relatives consequently sheds light on which sequences are essential.
The fundamental principle on which sequencing technology is based has essentially not changed since its development by Fred Sanger in 1977.
But which sequences satisfy that formula depends on which sequences that differ from the original at most on the variable in question satisfy the formula the quantifier embeds.
The latter is often limited by project funding, and the former may depend on which sequencing technology is promptly available.
One of the problems with identifying a putative crenarchaeal host using phylogenetics is that the final candidate ultimately depends on which sequences are chosen for analyses.
If library creation bias had a big effect on which sequences (of either size) were captured, we would see similar ranges of variability in both.
The choice of algorithm for assigning sequences to OTUs can also have a large impact on which sequences are clustered into the same OTU and on how many OTUs are observed in a study.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com