Package: msa 1.37.0

Ulrich Bodenhofer

msa: Multiple Sequence Alignment

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

Authors:Enrico Bonatesta [aut], Christoph Kainrath [aut], Ulrich Bodenhofer [aut,cre]

msa_1.37.0.tar.gz
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msa.pdf |msa.html✨
msa/json (API)
NEWS

# Install 'msa' in R:

install.packages('msa', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ubod/msa/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:msa-1.37.0(bioc 3.20)msa-1.36.0(bioc 3.19)

bioconductor-package

13 exports 2.42 score 19 dependencies 6 dependents 50 mentions

Last updated 2 months agofrom:dc8b00f4b2

Exports:msa msaCheckNames msaClustalOmega msaClustalW msaConsensusSequence msaConservationScore msaConvert msaMuscle msaPrettyPrint params print show version

Dependencies:askpass BiocGenerics Biostrings crayon curl GenomeInfoDb GenomeInfoDbData httr IRanges jsonlite mime openssl R6 Rcpp S4Vectors sys UCSC.utils XVector zlibbioc

msa - An R Package for Multiple Sequence Alignment

Rendered frommsa.Rnwusingknitr::knitron Jun 24 2024.

Last update: 2024-04-25
Started: 2015-04-10

Citation

Development and contributors

Readme and manuals

Help Manual

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