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Background: Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maximum likelihood., Results: We developed a novel program, named PQ, for reconstructing protein and nucleic acid phylogenies following a new character-based principle. Being tested on natural sequences PQ improves upon the results of maximum parsimony and maximum likelihood. Working with alignments of 10 and 15 sequences, it also outperforms the FastME program, which is based on one of the distance-based principles. Among all tested programs PQ is proved to be the least susceptible to long branch attraction. FastME outperforms PQ when processing alignments of 45 sequences, however. We confirm a recent result that on natural sequences FastME outperforms maximum parsimony and maximum likelihood. At the same time, both PQ and FastME are inferior to maximum parsimony and maximum likelihood on simulated sequences. PQ is open source and available to the public via an online interface., Conclusions: The software we developed offers an open-source alternative for phylogenetic reconstruction for relatively small sets of proteins and nucleic acids, with up to a few tens of sequences.