Tree quality on gap parsimony trees. Parsimony trees built from only gap information are used to evaluate the quality of MSAs. In the same manner as in the previous figure the relative Robinson-Foulds distance to a reference tree is measured and minus signs indicate a significant difference to Prank, which is always the best tool in this test, followed by ProGraphMSA. This indicates that phylogeny-aware gap placement  indeed produces phylogenetically more sensible gap patterns.
Szalkowski BMC Bioinformatics 2012 13:129 doi:10.1186/1471-2105-13-129