  In this paper, we present a toolbox for a specific optimization problem that
frequently arises in bioinformatics or genomics. In this specific optimisation
problem, the state space is a set of words of specified length over a finite
alphabet. To each word is associated a score. The overall objective is to find
the words which have the lowest possible score. This type of general
optimization problem is encountered in e.g 3D conformation optimisation for
protein structure prediction, or largest core genes subset discovery based on
best supported phylogenetic tree for a set of species. In order to solve this
problem, we propose a toolbox that can be easily launched using MPI and embeds
3 well-known metaheuristics. The toolbox is fully parametrized and well
documented. It has been specifically designed to be easy modified and possibly
improved by the user depending on the application, and does not require to be a
computer scientist. We show that the toolbox performs very well on two
difficult practical problems.
