Multiple Sequence Alignment


[Up] [Top]

Documentation for package ‘msa’ version 1.12.0

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'