To determine whether spindly HA phylogenies, co-circulation of antigenic variants, and high annual attack rates indeed come out of a model that incorporates deleterious mutations, we implemented a phylodynamic model that simulates the occurrence of both non-antigenic (largely deleterious) mutations and antigenic mutations ('Materials and methods').
To confirm whether or not the properties can be used as criteria for distinguishing LoF and GoF mutations, we implemented a classification technique using the support vector machine, random forest, and linear logistic regression methods with 50 data sets which contain equal numbers of LoF and GoF mutations to avoid bias.
A mutation tool named AjMutator [20] implements a subset of our pointcut-related operators [12].
To explore the full evolutionary dynamics of our model with non-antigenic and antigenic mutations, we implemented an individual-based model that allowed for an arbitrary number of new strains to enter the population and co-circulate.
The N-queens problem was used specifically to test the accuracy of the new adaptive mutation rate since a GA implementing a constant mutation rate does not have 100% accuracy in the N-queens problem.
The only mutations implemented are substitutions, which happen with a per base probability μ.
Updating matrices of a solution after implementing a mutation operator has been another difference.
Contrarily, taking into consideration the weakness of existing greedy strategies, [16] introduced a new differential evolution (DE) algorithm, named JADE, to improve optimization performance by implementing a new mutation strategy "DE/current-to-pbest" with optional external archive and updating control parameters in an adaptive manner.
The current version of Mutation@A Glance does not implement a method for quantitative evaluation of mutation effects on RNA splicing, mainly because we considered the evaluation method is not matured enough yet.
Based on our findings, a simple approach for improving the reliability of lower confidence somatic mutations would be to implement an additional program.
