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Relationship of alignment accuracy and sequence identity. (A) Proportion of sites correctly aligned versus true percent identity among the sequences. (B) Proportion of sites correctly aligned versus observed percent identity after alignment. (C) Observed versus true percent identity. JC = Jukes-Cantor model [37]; HKY = Hasegawa-Kishino-Yano model [38]; HKY + Γ = Hasegawa-Kishino-Yano plus gamma-distributed rates model. All points represent the average of 1000 simulation replicates.
