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| msa-package | Multiple Sequence Alignment |
| class:MsaAAMultipleAlignment | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| class:MsaDNAMultipleAlignment | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| class:MsaMetaData | Class 'MsaMetaData' |
| class:MsaRNAMultipleAlignment | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| msa | Unified interface to multiple sequence alignment algorithms |
| MsaAAMultipleAlignment | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| MsaAAMultipleAlignment-class | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| msaCheckNames | Check and fix sequence names |
| msaClustalOmega | Multiple Sequence Alignment with ClustalOmega |
| msaClustalW | Multiple Sequence Alignment with ClustalW |
| msaConsensusSequence | Computation of Consensus Sequence from Multiple Alignment |
| msaConsensusSequence-method | Computation of Consensus Sequence from Multiple Alignment |
| msaConservationScore | Computation of Conservation Scores from Multiple Alignment |
| msaConservationScore-method | Computation of Conservation Scores from Multiple Alignment |
| msaConvert | Convert Multiple Sequence Alignment for Other Packages |
| MsaDNAMultipleAlignment | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| MsaDNAMultipleAlignment-class | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| MsaMetaData | Class 'MsaMetaData' |
| MsaMetaData-class | Class 'MsaMetaData' |
| msaMuscle | Multiple Sequence Alignment with MUSCLE |
| msaPackage | Multiple Sequence Alignment |
| msaPrettyPrint | Pretty-Printing of Multiple Sequence Alignments |
| MsaRNAMultipleAlignment | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| MsaRNAMultipleAlignment-class | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| params-method | Class 'MsaMetaData' |
| params-method | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| print-method | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| show-method | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |
| version | Class 'MsaMetaData' |
| version-method | Class 'MsaMetaData' |
| version-method | Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment', and 'MsaRNAMultipleAlignment' |