The main existing methods for reconstructing phylogenetic trees are based on maximum likelihood, Bayesian inference, maximum parsimony or distance. There are many distance based programs for phylogenetic trees reconstruction. The five most important distance based programs were selected: NJ, BioNJ, UPGMA, Weighbor and FastME. Synthetic data sets were applied in order to evaluate the distance-based methods under consideration. Then, the tool DiGrafu was developed, so as to exploit the best characteristics of these programs. Besides, the validation of this proposed solution was presented using real data.