For less diverse alignments, any MSA analysis will have a higher probability of predicting false positives (false SDPs, in this case) as a result of less discriminatory conservation scores.
In order to make fair comparisons among the diverse range-bin alignment techniques, in this paper we always use the method in [16] for the phase adjustment step.
Significant effects are more likely in participants with evidence of varus malalignment, rather than in a diverse cohort where alignment is likely to range from valgus (in which lateral wedges could be detrimental) to neutral to varus.
The taxa in M become more diverse if the alignment scores are inaccurate ultrametric distance estimates, if the species subtree's topology deviates from the respective part of the taxonomy or if the gene tree's topology deviates from the species tree, for instance due to varying rates of evolution or the inclusion of non-homologous segments in the analysis.
Here, we present INTREPID an information theoretic approach for functional site identification that exploits the information in large diverse multiple sequence alignments (MSAs).
Sequence alignment of diverse papillomavirus types shows that C22 and C28 of HPV16 L2 are absolutely conserved throughout the Family Papillomaviridae (Fig. 1A), prompting us to further examine the role of these two cysteines in HPV infection.
We generated a multiple alignment of diverse Aspergillus genomes with an average pairwise sequence identity of 58%, which is close to the optimal level of sequence identity for searching for RNAs.
The primers, listed in the legend to Table 1, were designed using the full-length genome alignment of diverse group M HIV-1 strains from the HIV sequence database [2].
The method could be applied for the instances located in modules whose multiple sequence alignment is diverse, such that the frequencies of amino acids at some positions are near to their mean values in all proteins, i.e. those positions are poorly conserved.
An alignment of diverse eukaryotic Rpn12 sequences defines 27 completely conserved residues (Supplementary Figure S2).
