Phylogenetic accuracy and the retention of sequences. A. Distribution of standardized quartet distances between estimated phylogenies and the corresponding true trees. Leftmost column: full alignments with no gap pattern applied. Green: gap pattern applied, phylogeny inferred directly (without the use of masking or SIA). Red: alignment masking. Blue: SIA. B. Proportion of sequences retained per family. Boxplots show the median (horizontal black bar) and interquartile range (colored boxes).