Flowchart of simulation and phylogenetic reconstruction process. Simulation of 2000 replicates of sequence sets was performed along the reference trees with an ancestral ITS2 sequence. Out of these, 1000 sequence-structure, sequence and concatenated sets were generated. Multiple sequence alignments were created for each of these sets and evolutionary distances were estimated with Profile Neighbor Joining. Resulting trees were afterwards compared with the reference trees and regarding their bootstrap support values. Q
are the substitution models for unpaired and paired regions, respectively.