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Base code and container build repository for the Salmon Algorithm and basic DNA Fragment Assembly benchmark problems

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The Salmon Algorithm

The Salmon Algorithm, developed by John Orth as part of his Master’s thesis, combines concepts from existing metaheuristics such as Genetic Algorithms(GA) and Ant Colony Optimization (ACO), to solve combinatorial optimization problems in a reasonable amount of time [1]. The Salmon Algorithm was inspired by the behaviour of salmon swimming upstream to spawn. In the wild, salmon return to the place they were born to spawn, suggesting something resembling a memory of the path their parents’ took. A salmon’s memory can be likened to parent chromosomes in GA, since both contain the full path of the parent. The memory parameter determines to what degree a salmon follows its parent’s path. Likewise, salmon will not lay eggs if the water level is too low. The water level can be likened to that of the pheromone which helps direct an ant’s path in ACO. Like many evolutionary algorithms, the salmon algorithm involves populations of salmon that run for several generations. The salmon algorithm makes no claims of accurately representing real salmon, but attempts to simulate idealized aspects of salmon’s spawning behaviour to effectively solve computationally hard problems [1].

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1. J. Orth, “The Salmon Algorithm-A New Population Based Search Metaheuristic,” Master’s Thesis, Brock University, 2012. [Online]. Available: https://dr.library.brocku.ca/handle/10464/3929

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