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This system allows rapid implementation of heuristics approximating to many complex alignment models, and has been incorporated into the freely available sequence alignment program, exonerate.
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Guy Slater
Ewan Birney
BMC Bioinformatics
SHILAP Revista de lepidopterología
Wellcome Trust
European Bioinformatics Institute
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Slater et al. (Tue,) studied this question.
www.synapsesocial.com/papers/69d98ef22a25b240b7a3ce4c — DOI: https://doi.org/10.1186/1471-2105-6-31