<p>(A) Violin graphs showing the distribution of paired differences of the RF distances between the resulting trees generated by TIPars and UShER (TIPars—UShER) for the random 100 and 1000 multiple sequences insertions. (B) Violin graphs showing the distribution of paired differences of the Gamma20 log-likelihoods between the resulting trees generated by TIPars and UShER (TIPars—UShER) for the random 100 and 1000 multiple sequences insertions. (C) Violin graphs showing the distribution of paired differences of the RF distances between the resulting trees generated by TIPars and UShER (TIPars—UShER) for the successive 100 and 1000 multiple sequences insertions. (D) Violin graphs showing the distribution of paired differences of the Gamma20 log-likelihoods between the resulting trees generated by TIPars and UShER (TIPars—UShER) for the successive 100 and 1000 multiple sequences insertions. (E) Distribution of paired differences in the RF distances between the resulting trees generated by TIPars and UShER (TIPars—UShER) on 16S, H3N2 and NDV random 50 multiple sequences insertions. (F) Distribution of the paired differences in the Gamma20 log-likelihoods between the resulting trees generated by TIPars and the four other programs (TIPars—Others) on 16S random 50 multiple sequences insertions. (G) Distribution of the paired differences in the Gamma20 log-likelihoods between the resulting trees generated by TIPars and the four other programs (TIPars—Others) on H3N2 random 50 multiple sequences insertions. (H) Distribution of the paired differences in the Gamma20 log-likelihoods between the resulting trees generated by TIPars and the four other programs (TIPars—Others) on NDV random 50 multiple sequences insertions. P-values for the right-sided paired t-tests are indicated by the asterisk on top of each violin diagram, where p<0.05 is indicated by one pink asterisk (*), p<0.01 by two orange asterisks (**) and p<0.001 by three red asterisks (***).</p>