When two species are regarded as heterotypic synonyms, this does not affect the status of type strains as type strains. The type strain of the younger heterotypic synonym remains the type strain of the younger heterotypic synonym; it neither becomes the type strain of the older heterotypic synonym nor does it lose its status as type strain entirely. The TYGS aims at an unambiguous relationship between taxon names and type strains. For each type strain the taxon name (or set of taxon names) for which it is the type strain must be shown to achieve this, even if the taxon name is actually believed to be a younger heterotypic synonym and thus not believed to be the correct name. Notably, as specified in the International Code of Nomenclature of Prokaryotes, if alternatives are available the choice of the correct name depends on taxonomic opinion.
Moreover, the analyses conducted with the TYGS yield taxon boundaries themselves. Information on heterotypic synonyms is thus part of the outcome and should not be part of the input. Often the TYGS results simply confirm known synonym relationships. But surprises are also possible. Additional information on known heterotypic synonyms is available from LPSN, to which the TYGS results are linked. Heterotypic synonyms at the species or subspecies level may contain distinct genus names. To assess the affiliation to a genus it is necessary to consider the position of the type species of the genus.