In the top ranked model from the COT group, we observe a high correlation between the intrinsic hydrolysis rate and the maximum rate parameter in the Michaelis-Menten term values in both the GAP5 and the GAP7 functions.
In the top-ranked model, there is high correlation between the estimated values of the parameters of the auto-catalysis component of GEF7 and between the estimated values of the GAP7 intrinsic hydrolysis rate and the maximum rate parameter in the Michaelis-Menten term.
There were no significant differences in maximum growth rate (parameter c; Figure 2) between salinities or between populations (Additional file 1: Table S3 and Figure 3c).
We approach the quasispecies as an ecosystem, what implies that the fitness of each viral phenotype or virus variant results from the combination of its intrinsic properties (collected in a maximum growth rate parameter) and those resulting from its interactions (interaction coefficients, negative in the case of competition and positive for cooperation) with the other variants.
We do this using Hill functions [27], or
The time complexity scales exponentially with the factor graph degree, which is defined as the maximum number of variable nodes adjacent to any factor node, or the maximum number of unknown rate parameters appearing in any ODE.
This method calculates maximum likelihood estimates of speciation rate parameters and a likelihood score per tree.
Methods used to determine these reaction rate parameters include maximum likelihood ratio [ 8- 10], gradient decent [ 11], and moment closure [ 12].
The hyperparameters (a ^, b ^ ) are found via maximum likelihood estimation given relative rate parameters (r ^, p → ^, λ → ^, ϵ → ^ and δ ^ ).
In these analyses, the GTR model was generally applied, with partition-wide estimates of the rate parameters by maximum likelihood optimization and empirical nucleotide frequency parameters.
