Infernal 1.0: inference of RNA alignments

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How researchers see this paper

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Ecology and exploration of the rare biosphere (2015, methodology): “Aligning to a structural model using programmes such as Infernal 178 and SINA 179 , or tools at the Comparative RNA Web Site 180 , enables divergent but valid sequences to persist.”
Rfam: Wikipedia, clans and the “decimal” release (2010, methodology): “These are used to build CMs, statistical models of a family’s conserved sequence and secondary structure, using the Infernal suite of analysis tools (9).”
ViennaRNA Package 2.0 (2011, methodology): “As an alternative to the direct measurement of thermodynamic parameters, for instance, machine learning approaches employing stochastic context free grammars (SCFG) were introduced e.g. in the infernal suite [16,17].”
nhmmer: DNA homology search with profile HMMs (2013, positive): “The core pipeline of nhmmer has also been incorporated as an acceleration filter for the RNA homology search tool Infernal, where it supports fast filtering with negligible loss in Infernal sensitivity (E.Nawrocki and S.R.Eddy, unpublished data).”