Infernal 1.1 is a software tool for RNA homology search and alignment, significantly faster than previous versions. It uses covariance models (CMs), which are probabilistic models of RNA sequence and secondary structure. Infernal 1.1 introduces a new filter pipeline based on accelerated profile HMM methods and HMM-banded CM alignment methods, enabling up to 100-fold acceleration over version 1.0.2 and 10,000-fold acceleration over non-filtered CM searches. The software is freely available under the GNU GPLv3 license and is portable to any POSIX-compliant operating system. Infernal 1.1 improves search speed by using profile HMM filters and banded CM alignment methods. These methods reduce the number of calculations required, making the search process faster without sacrificing sensitivity. The new filter stages are sufficiently fast that the post-HMM-filtering CM dynamic programming (DP) algorithms became the computational bottleneck. To address this, constraints (bands) derived from HMM alignments are imposed on the DP matrices, significantly reducing the number of calculations. The software has two main applications: searching for structural RNAs in sequence datasets and creating multiple sequence- and structure-based alignments of RNA homologs. Both applications begin with a CM file, which can be downloaded from the Rfam database or created using Infernal's cmbuild program. Before a CM can be used to search a sequence database, it must be calibrated using the cmcalibrate program. Infernal 1.1 performs benchmark searches in 0.44 hours, which is about 100 times faster than the previous version (1.0.2) and 10,000 times faster than non-filtered searches. The software is now a more practical tool for RNA homology search, enabling its incorporation into automated sequence annotation pipelines and reducing the need for additional filtering schemes. The most expensive programs (cmalign, cmcalibrate, cmscan, and cmsearch) are implemented for use with multiple threads on multi-core machines and in coarse-grained MPI versions for clusters.Infernal 1.1 is a software tool for RNA homology search and alignment, significantly faster than previous versions. It uses covariance models (CMs), which are probabilistic models of RNA sequence and secondary structure. Infernal 1.1 introduces a new filter pipeline based on accelerated profile HMM methods and HMM-banded CM alignment methods, enabling up to 100-fold acceleration over version 1.0.2 and 10,000-fold acceleration over non-filtered CM searches. The software is freely available under the GNU GPLv3 license and is portable to any POSIX-compliant operating system. Infernal 1.1 improves search speed by using profile HMM filters and banded CM alignment methods. These methods reduce the number of calculations required, making the search process faster without sacrificing sensitivity. The new filter stages are sufficiently fast that the post-HMM-filtering CM dynamic programming (DP) algorithms became the computational bottleneck. To address this, constraints (bands) derived from HMM alignments are imposed on the DP matrices, significantly reducing the number of calculations. The software has two main applications: searching for structural RNAs in sequence datasets and creating multiple sequence- and structure-based alignments of RNA homologs. Both applications begin with a CM file, which can be downloaded from the Rfam database or created using Infernal's cmbuild program. Before a CM can be used to search a sequence database, it must be calibrated using the cmcalibrate program. Infernal 1.1 performs benchmark searches in 0.44 hours, which is about 100 times faster than the previous version (1.0.2) and 10,000 times faster than non-filtered searches. The software is now a more practical tool for RNA homology search, enabling its incorporation into automated sequence annotation pipelines and reducing the need for additional filtering schemes. The most expensive programs (cmalign, cmcalibrate, cmscan, and cmsearch) are implemented for use with multiple threads on multi-core machines and in coarse-grained MPI versions for clusters.