| cm_5_8S | Covariance Model for 5.8S rRNA | 
| cmalign | Align sequences to a covariance model | 
| cmbuild | Construct covariance model(s) from structually annotated... | 
| cmcalibrate | Calibrate a covariance model for searching | 
| cmsearch | Search for Covariance Models (CM) in a set of sequences. | 
| read_stockholm_msa | Parse a Multiple Alignment in Stockholm Format | 
| sample_data | Sample rRNA sequences | 
| stk_5_8S | Annotated Seed Alignment for 5.8S rRNA | 
| StockholmMultipleAlignment-class | StockholmMultipleAlignment objects | 
| writeStockholmMultipleAlignment | Write an annotated alignment in Stockholm format | 
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