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In all experiments, the noise estimation in the decomposition levels was done using the heuristic variant of the Stein's unbiased rule.
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Parsimony analysis was conducted with the program PAUP* 4.0b10, using the heuristic search option [63].
The MP tree [ 68] was obtained using the heuristic search method.
The last two trees were obtained using the heuristic search algorithm.
The ML tree was implemented using the heuristic search option with TBR branch swapping.
The second goal was to use the heuristic genetic algorithm to discover new models exhibiting three-way epistasis for the genetic variants defined above from among the 25 possible combinations of mathematic functions.
This indicates the heuristic gives good results, and in the following, we use the heuristic solution for the three instances not solvable by ILP.
We use the heuristic algorithm proposed by (Andrews et al., 2003) to solve this problem.
FastTree 1.0 uses a heuristic variant of neighbor joining [3], [4] to quickly find a starting tree and uses nearest-neighbor interchanges (NNIs) to refine the topology.
MP bootstrap percentages were obtained after 1,000 replications using the same heuristic search strategy using Paup*.
When using the population heuristic, the disambiguator always chooses the most populated place.
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