ExAlt-Exon, ExAlt-Frame, and ExAlt-Default were compared to the respective ab initio equivalent: ExAlt-Exon-ab initio, ExAlt-Frame-ab initio, and ExAlt-Default-ab initio. Each ab initio version is the GHMM equivalent to the PGHMM using only the target D. melanogaster sequence as input. The multi-species versions of ExAlt in all cases reduced the number of false positive predictions over the equivalent ab initio version, with little or no reduction in sensitivity.