The most commonly used aligners have varying alignment quality and speed, tend to depend on a specific reference alignment, or lack a complete description of the underlying algorithm.
The accuracy values were calculated for threshold values of 95% query coverage and varying alignment identity.
Accuracy was used as measurement for the proportion of true classifications by DeconSeq and calculated for thresholds of 95% query coverage and varying alignment identity.
To evaluate the effect of varying alignment parameter values on cladogram topology, independent analyses of the complete data set were performed for a range of parameter combinations (sensitivity analysis sensu [ 103]) under parsimony.
We wanted to investigate what effect (if any) sequence length would have on amino acid model selection by performing the model selection procedure on varying length alignments.
Silicon nitride/hexagonal boron nitride (h-BN) functionally graded materials (FGMs) were fabricated by hot pressing at 1750°C for 2 h, varying the alignment of the amount of hexagonal BN using powder layering method.
Silicon nitride/hexagonal boron nitride (h-BN) ceramic composites and functionally graded materials were fabricated by hot pressing at 1750 °C for 2 h, varying the alignment of the amount of hexagonal BN using powder layering method.
Varying the alignment and reporting modes allowed the differential detection of two predominant peak sizes of sequencing reads as described in the results section.
These observations were further strengthened by the analysis of multiple ROC curves (Additional file 1: Figure S24) generated for multiple peptide lengths (31, 51 and 71aa) with varying range of alignment parameters (alignment coverage and identity levels).
In the following sections, we provide the results of simulations to investigate the effects of using varying base trees, alignments lengths, among-site rate variation (ASRV) parameters, and amino acid frequencies in amino acid alignments on the selection of protein models.
Comparison of different alignments varying for gap costs may be used to identify the most consistent significantly associated polymorphic sites.
