In light of the interest in ancestral genome reconstruction,
several authors have approached the problem of indel modeling from this slightly different direction.
Typically these approaches require the input alignment to be specified and this leads the authors to a slightly different formalism,
although the methods can still be reformulated within the framework of string transducers.
Alexandre Bouchard-Côté, Michael I. Jordan and Dan Klein. (2009) Efficient Inference in Phylogenetic InDel Trees. Advances in Neural Information Processing Systems 21 (NIPS). Vancouver, Canada. (paper)