Sentence examples for over alignments from inspiring English sources

Custom parameters estimated by e.g. expectation maximization over alignments of a given divergence range will supposedly perform even better.

A PHMM defines a probability distribution over alignments of two sequences X and Y.

To gain a better insight on selective pressure, we conducted analysis of ratios of dS, the number of synonymous substitutions per synonymous sites, to dN, the number of non-synonymous substitutions per non-synonymous sites, over alignments covering the entire LRR domain.

The methods do not rule out that over-alignment has lead to artifacts in the sub-tomogram averaging structures.

Intuitively, this ratio measures the average quality of the alignment over aligned and non-aligned sites.

It should be noted that we do not expect a better performance of LMS distances over alignment-based distances when comparing catalytic domains only.

The sum of all scores over alignment columns for a query pair of sequences serves as an approximation of the likelihood ratio statistic comparing the model of independence (null) with the model of homology (alternative).

In addition, for the most conserved Cons alignments (>86% identity over alignment length) the fraction of human-specific positively selected genes was very similar for Cons and PALO (∼0.7%) but still more than double for Longest (∼1.6%).

Quartets containing short internal branches (less than three substitutions over alignment length) or long external branches (10 times longer than internal branch) were excluded from analyses before the summarizing step.

Screening for diversifying selection over alignment positions was implemented with mixed effects model of evolution with default parameters, due to its ability of detecting episodic selection (Murrell et al. 2012).

The typical use case for modern likelihood-based inferences are so-called partitioned analyses, where subsets of the alignment sites form partitions that evolve under a distinct set of evolutionary model parameters (e.g. α shape parameter, GTR rates, base frequencies, etc).. ExaML parallelizes likelihood calculations over alignment sites using MPI (Message Passing Interface).