Fig. 2

The effects of alignment uncertainty and the choice of substitution models on species tree estimation. a The pairwise distances of the ASTRAL, concatenation, NJst, and STAR trees estimated from the BT, AT, FP, and FM alignments. b The pairwise distances of the ASTRAL, concatenation, NJst, and STAR trees estimated with the JC, K80, and GTR models. Note that the pairwise distances of the ASTRAL, NJst, and STAR trees are equal to 0