Can't speak for tmaly, but you might look at things like the Xerox Finite State Tools, Helsinki Finite State Tools, or KLEENE. They were developed with linguist

Can't speak for tmaly, but you might look at things like the Xerox Finite State Tools, Helsinki Finite State Tools, or KLEENE. They were developed with linguistics in mind, but are in fact general-purpose tools for generating and editing string-matching state machines. It seems like every time I learn something new about bioinformatics, it just has more and more overlap with computational linguistics!