“Overall the S(T) score of 0.990241 means that the computer believes it has figured out the structure nearly perfectly.”

in the posting by Angelo Embuldeniya above. It means that the
tree represents in a qualitative sense the relative distances
between the virii genomes
in the supplied distance matrix almost perfectly. This translates
into true relatedness among the virii insofar as the distances
have captured it. The used distance is NCD which has previously successfully determined phylogeny trees from the full mtDNA of
species like mammals and fungi. So there is reason to believe its
output is dependable but it is certainly not infallible. In that
sense the NCD distance is comparable to allignment distance, but
it is less sensitive to position of substring sequences in the
sequence.