Infernal 1.1 is an updated version of the RNA homology search tool, which builds covariance models (CMs) from structurally annotated multiple sequence alignments. This version introduces a new filter pipeline based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods, achieving a ~100-fold acceleration over the previous version and a ~10,000-fold acceleration over exhaustive non-filtered searches. The new filters and banded CM methods significantly reduce computational time without compromising sensitivity. Infernal 1.1 is available for download and is freely licensed under the GNU GPLv3, making it accessible to researchers for various applications, including genome annotation and environmental survey studies. The tool's performance is validated through benchmarking, demonstrating its efficiency and practicality for large-scale RNA homology searches.Infernal 1.1 is an updated version of the RNA homology search tool, which builds covariance models (CMs) from structurally annotated multiple sequence alignments. This version introduces a new filter pipeline based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods, achieving a ~100-fold acceleration over the previous version and a ~10,000-fold acceleration over exhaustive non-filtered searches. The new filters and banded CM methods significantly reduce computational time without compromising sensitivity. Infernal 1.1 is available for download and is freely licensed under the GNU GPLv3, making it accessible to researchers for various applications, including genome annotation and environmental survey studies. The tool's performance is validated through benchmarking, demonstrating its efficiency and practicality for large-scale RNA homology searches.