Schematic of the phylogeny-based tests of alignment accuracy. Both tests are based on large-scale genomic data: (a) The species-tree discordance test samples sets of orthologs inferred by OMA among species with a well-accepted phylogeny (Additional file 1, Figure S1). Each sample is aligned by the different packages. The resulting alignments are evaluated by reconstructing trees from them, and comparing with the reference topology. All else being equal, trees from better alignment packages show higher average congruence with the reference topology. (b) The minimum duplication test follows a similar idea, but differs from the first test in two ways. First, it samples sets of homologs rather than the more specific orthologs. Second, the evaluation is based on a parsimony argument rather than knowledge about the phylogeny of the species: all else being equal, alignments yielding trees with fewer duplication nodes on average are more accurate.
Dessimoz and Gil Genome Biology 2010 11:R37 doi:10.1186/gb-2010-11-4-r37