Boolean analysis (or BOOL-AN; Jakó et al., 2009. BOOL-AN: A method for 
comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. 
Evol. 52, 887-97.), a recently developed method for sequence comparison uses the 
Iterative Canonical Form of Boolean functions. It considers sequence information 
in a way entirely different from standard phylogenetic methods (i.e. Maximum 
Parsimony, Maximum-Likelihood, Neighbor-Joining, and Bayesian analysis). The 
performance and reliability of Boolean analysis were tested and compared with 
the standard phylogenetic methods, using artificially evolved - simulated - 
nucleotide sequences and the 22 mitochondrial tRNA genes of the great apes. At 
the outset, we assumed that the phylogeny of Hominidae is generally well 
established, and the guide tree of artificial sequence evolution can also be 
used as a benchmark. These offer a possibility to compare and test the 
performance of different phylogenetic methods. Trees were reconstructed by each 
method from 2500 simulated sequences and 22 mitochondrial tRNA sequences. We 
also introduced a special re-sampling method for Boolean analysis on permuted 
sequence sites, the P-BOOL-AN procedure. Considering the reliability values 
(branch support values of consensus trees and Robinson-Foulds distances) we used 
for simulated sequence trees produced by different phylogenetic methods, BOOL-AN 
appeared as the most reliable method. Although the mitochondrial tRNA sequences 
of great apes are relatively short (59-75 bases long) and the ratio of their 
constant characters is about 75%, BOOL-AN, P-BOOL-AN and the Bayesian approach 
produced the same tree-topology as the established phylogeny, while the outcomes 
of Maximum Parsimony, Maximum-Likelihood and Neighbor-Joining methods were 
equivocal. We conclude that Boolean analysis is a promising alternative to 
existing methods of sequence comparison for phylogenetic reconstruction and 
congruence analysis.