Abstract
One of the many problems that are considered to be NP-Hard is the Multiple Sequence Alignment one that initially requires, as for any other of its siblings, a specific encoding schema and design of the main functionalities of the heuristics algorithm being implemented and executed. This paper intends to discuss our proposed generic implementation of the Simulated Annealing, inspired for the procedure of cooling and shaping methods of metals. In our algorithm, we attempted to add some executions tracing functionalities in order to help later analysis for initial parameters tuning. On another hand, we also tried to get closer in our attempt to mimic the cooling of metals, but giving it an option to run under different cooling schedules. We proposed a few schedules that seemed to be studied and/or used in many algorithm implementations.
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