The CMCompare program takes two Infernal covariance models and calculates the Link sequence and its Link score. The Link sequence is the sequence scored by both models highest at the same time. Two models with a high Link score are not well separated from each other.
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Discriminatory power of RNA family models
Höner zu Siederdissen, Christian and Hofacker, Ivo L.
Bioinformatics, 2010, 26, 453-459