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The probabilities of mutation and crossover were 0.15 and 0.8, respectively.
Probabilities of mutation frequency differences were calculated using Poisson distribution.
When a given classification algorithm produced posterior probabilities of mutation status, we assigned each variant's mutation status according to the higher posterior probability (Weka's default behavior).
Probabilities of mutation can also be incorporated.
This is an issue that deserves further investigation and one possible reason may be due to increasing inaccuracy of approximating the larger probabilities of mutation patterns used in the likelihood analysis.
Interestingly, it is possible to observe such conservation pattern in the model with an identical probabilities of mutation and fixation for all non-consensus nucleotides in all orthologous site rows, with a single preferred nucleotide, the consensus, the same in all sites.
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These models build on two separate parameters for a newly arisen mutant allele: the probability of mutation (effect of mutational bias or mutating tendency towards the mutated nucleotide) and the probability of fixation (effect of selection coefficients).
Moreover, they have found no evidence that this association is mediated through fixation probabilities of mutations.
For each residue, a 20-dimensional vector was calculated to denote the conservation probabilities of mutations to 20 basic amino acids.
We multiplied individual probabilities of mutations within a scenario to calculate the overall relative probability (ORP) that an environmental isolate was related to the infection source (Table 2; Figure 2).
(P_{M}) Probability of mutation operator that represents the number of chromosomes mutating in each iteration of algorithm.
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