Phylogeny-aware alignment with PRANK

Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary and structural homology are not the same and sequence alignments generated with methods designed for structural matching can be seriously misleading in comparative and phylogenetic analyses. The phylogeny-aware alignment algorithm implemented in the program PRANK has been shown to produce good alignments for evolutionary inferences. Unlike other alignment programs, PRANK makes use of phylogenetic information to distinguish alignment gaps caused by insertions or deletions and, thereafter, handles the two types of events differently. As a by-product of the correct handling of insertions and deletions,…