3. Current Quirks

• Standalone direct DUMMEST invocation (running the underlying aligner directly instead of the dummest command) is not well tested at present. Using the dummest command is preferred, including when running in --max mode.
• The tool might not be suitable for short sequences or profiles because DUMMEST does not implement the additional short-sequence corrections that HMMER3 and BATH use.
• There is currently no way to estimate frameshift probability parameters from sequences like in last-train. Instead, DUMMEST uses a fixed default set of frameshift (indel) rates approximated from Badread's nanopore2020 error model (ONT R9.4.1) at 90% target identity; see docs/frameshift-rate-approximation.md.