Comparison of distance matrices for primate mitochondrial genomes. We applied various alignment-free methods to a set of 27 mitochondrial genomes from different primates and compared the resulting distance matrices to a trusted reference distance matrix using the Mantel test. The similarity between the calculated matrices and the reference matrix is plotted. We applied our Spaced-Words approach using sets of 100 randomly calculated patterns with weight k=9 and length ℓ between 9 and 39, i.e. with 9 match positions and up to 30 don’t care positions. Yellow squares are the results for the ‘binary’ version of new distance measure
. We did not use the reverse-complement option on these data, since genes in the compared genomes are known to be on the same strand. Green diamonds are the results for the Jensen-Shannon distance applied to the same spaced-word frequency vectors as explained in . In addition, distances calculated by six other alignment-free methods were evaluated.