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We can view these two sets of sites as evolving independent of each other.
The raw ITC curves were best fitted to two sets of sites binding model.
Mutual information assesses the degree to which the variability between the two sets of sites treated individually exceeds their variability when considered collectively.
Data were fitted to the two sets of sites model according to the user's manual for the VP-ITC microcalorimeter, where a Kd value of 1.4 nM was fixed for the first site.
The process of adding substitutions to the two sets of sites is independent of each other (except in one case, when the substitution rates were set to be correlated see below).
In a first approach we compared the likelihood of a model (M1a) that assumes two sets of sites with neutral (ω = 1) or nearly neutral evolution (0 < ω < 1), to a model (M2a) with an additional class of sites with ω > 1 (modelmodel = 0 and NSsites = 1; modelmodel = 0 and NSsites = 2).
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We used the two-sample Kolmogorov Smirnov test to compare distributions of Kr in two sets of site-genome pairs.
Two sets of site models are commonly used to test hypotheses of selection, and have been used here: M1a vs. M2a and M7 vs. M8.
The two sets of site-specific likelihood values were imported into a standard database program, and relative support for the two models at each site, i, was measured as the difference in natural log-likelihood values at that site, ΔlnL i.
The results obtained under the two sets of site models (M1a vs. M2a and M7 vs. M8) differ in some aspects; for example, the more conservative M1a vs. M2a comparison did not reveal statistically significant results for CCR2 while the M7 vs. M8 comparison did reveal significant differences, allowing for the identification of positively selected sites.
In this analysis, we considered seven sets of sites that were created by successive elimination of sites with the highest substitution rate in the given set.
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