On the avian dataset, we ran ASTRAL, ASTRID, and DISTIQUE-8 and used both bootstrapping  and local posterior probability (pp)  to quantify branch support (Additional file 1: Figures S8 and S9). Bootstrap support was generally high, but the local pp was low for many branches. DISTIQUE and ASTRID differed on three branches. Of these, one, related to the first neoavan split, had high local pp support in ASTRID (0.98) but very low local pp in DISTIQUE; the remaining conflicts had local pp below 0.58 in both trees. ASTRAL and DISTIQUE differed in six branches, and all of these had local pp below 0.58 in DISTIQUE, and all but one also had low local pp (≤ 0.9) in ASTRAL. None of these conflicting relationships have been well resolved in the literature. Interestingly, many of conflicting branches with low local pp had high bootstrap support. It can be argued that conflicts are due to uncertainties resulting from insufficient data, but bootstrapping misleadingly computes high support .