# Multiple Sequence Alignment

## Documentation for package ‘msa’ version 1.15.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'