SHIRO is a set of tools based on HSMM (Hidden Semi-Markov Model), for aligning phoneme transcription with speech recordings, as well as training phoneme-to-speech alignment models.

Blatantly I created SHIRO because there seems to be no open-source alternatives to HTK available for automatic phoneme alignment. Though by no means SHIRO can be a completely replacement for HTK, which also does speech recognition and language modeling, SHIRO is useful for what it's designed for.

Donald Trump Hillary Clinton HTK SHIRO
Big Mouth
Crooked ?
Costs $$$
Supports both LRHMM and LRHSMM-based speech alignment with multi-state, multi-stream GMM and arbitrary state tying and allows client-side deployment.