- Plan7 HMMER support: full Plan7 architecture with single-hit (
--hmmer-plan7) and multi-hit (--hmmer-multihit) modes - Python/JAX package (
machineboss): machine construction, weight algebra, evaluation, Forward/Backward/Viterbi on GPU via JAX - Fused Plan7+transducer algorithms (GeneWise-style) avoiding explicit state-space composition
- CLI (
boss): transducer construction, composition, intersection, concatenation, union, Kleene closure - Forward, Backward, and Viterbi algorithms
- Baum-Welch training via GSL optimizers
- Beam search encoding/decoding
- CTC prefix search, MCMC, simulated annealing decoding
- Code generation (C++/JS) for Forward algorithm
- HMMER profile HMM import
- CSV profile import
- Regular expression construction
- Preset machines (translate, dnapsw, protpsw, Jukes-Cantor, TKF91, Hamming codes, etc.)
- JSON schema validation
- GraphViz DOT output