Data from: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Multiple sequence aligners typically work by progressively aligning the
most closely related sequences or group of sequences according to guide
trees. In PNAS, Boyce et al. report that alignments reconstructed using
simple chained trees (i.e., comb-like topologies) with random leaf
assignment performed better in protein structure-based benchmarks than
those reconstructed using phylogenies estimated from the data as guide
trees. The authors state that this result could turn decades of research
in the field on its head. In light of this statement, it is important to
check immediately whether their result holds under evolutionary criteria:
recovery of homologous sequence residues and inference of phylogenetic
trees from the alignments. We have done this and the results are entirely
opposed to Boyce et al.’s findings.