Figure 5.

Tree quality as proxy for MSA quality. Tree quality as proxy for MSA quality measured as Robinson-Foulds distance (divided by maximum possible distance) of reconstructed PhyML tree to a reference tree. We observe that particularly ProGraphMSA D using the Darwin model is among the best tools in all data sets. A minus sign indicates a significant difference to the best tool using a Wilcoxon signed-rank test. Please note that the vertical axis does not start at zero to highlight the rather mild differences in performance.