Generalized Pair HMM
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Generalized pair hidden Markov models:
- Majoros et al.: Efficient implementation of a generalized pair hidden Markov model for comparative gene finding. Bioinformatics 2005;21:1782-8.
- Alexandersson et al.: SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res. 2003;13:496-502.
- Pachter et al.: Applications of generalized pair hidden Markov models to alignment and gene finding problems. J. Comput. Biol. 2002;9:389-99.
See also the Long Indel Model, which introduces realistic indel length distributions to the TKF model:
- Miklós et al.: A "Long Indel" model for evolutionary sequence alignment. Mol. Biol. Evol. 2004;21:529-40.
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