Nowadays, Multiple Sequence Alignment (MSA) approaches do not always provide consistent solutions. In fact, alignments become increasingly difficult when treating low similarity sequences. Tabu Search is a very useful meta-heuristic approach in solving optimization problems. For the alignment of multiple sequences, which is a NP-hard problem, we apply a tabu search algorithm improved by several neighborhood generation techniques using guide trees. The algorithm is tested with the BAliBASE benchmarking database, and experiments showed encouraging results compared to the algorithms studied in this paper.