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Genotype data under different selection strength and neutral selection generated by SelSim were mixed together [ 27], then the empirical distribution method was applied to find outliers.
Otsu, N. A threshold selection method from gray-level histograms.
data-mining selection method.
Our novel selection method addresses these points.
Values significantly ≪1.0 indicate purifying selection, whereas neutral selection theoretically yields a value of ∼1.0.
The log-likelihood values from the M1a (neutral selection) and M2a (positive selection) models and the M7 (neutral selection) and M8 (positive selection models were used to perform a likelihood ratio test (LRT).
The Dn/Ds ratio of the concatenated MLST sequences yielded 0.0588, indicating neutral selection.
Dn/Ds < or = 1 indicates purifying or neutral selection, favouring amino acid substitutions [26].
Ka/Ks ratio >1, <1 and =1 represent positive selection, purifying selection and neutral selection, respectively.
pi (N): proportion of sites undergoing neutral selection.
A value of 0 indicates the presence of neutral selection.
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