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szhan committed Jun 19, 2024
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Expand Up @@ -16,12 +16,16 @@ Note that there are two special values `NONCOPY` and `MISSING`. `NONCOPY` (or `-
* Recombination probabilities.
* Mutation probabilities.

### Algorithms
* Forward-backward algorithm using the haploid LS HMM.
* Viterbi algorithm using the diploid LS HMM.
### Models and algorithms
* Haploid LS HMM
* Forward-backward algorithm
* Viterbi algorithm
* Diploid LS HMM
* Forward-backward algorithm
* Viterbi algorithm

### Features
* Scaling of mutation rate by the number of distinct alleles per site.
* Non-copiable state in the reference panel (`NONCOPY`).
* Missing state in the query (`MISSING`).
* Multiallelic sites.
* Multiallelic sites (haploid only).

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