Accuracy in phylogenetic inference. Comparison of phylogenetic accuracy obtained with different data sets. Accuracy is measured as tree similarity between the true tree (used for simulating the data set) and the reconstructed tree. Each line shows the distribution of the accuracy results from 1000 different data sets, in the form of a box plot. The box has lines at the lower quartile, median and upper quartile. The whiskers extend from each quartile to the most extreme values within 1.5 times the interquartile range. Outliers falling outside this range are marked with dots. The datasets are in the same order (from top to bottom) as in table 2: The top two rows show the original dataset without and with removal of gapped columns, respectively. The third and fourth rows show the equivalent MaxAlign datasets. The trees in the top four rows are being evaluated on the subset of sequences shared by all data sets ("Subset"), while the lower two rows show the results for original datasets when evaluated on the full set of sequences ("All").