Evaluation of the salmon algorithm

Abstract

The salmon algorithm is a metaheuristic inspired by the behaviour of salmon swimming upstream to spawn. It has previously shown success when used for the creation of sets of robust tags for DNA sequencing applications, as well as for the travelling salesman problem. In this paper the salmon algorithm is evaluated for the construction of optimal covering and error-correcting codes, which are related to sequencing applications, as well as for the DNA fragment assembly problem, which is related to the travelling salesman problem. Parameter tuning for the salmon algorithm is extensively studied, as well as the use of automated parameter tuning.