Package: msa 1.45.1

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, ths]

msa_1.45.1.tar.gz
msa_1.45.1.zip(r-4.7)msa_1.45.1.zip(r-4.6)msa_1.45.1.zip(r-4.5)
msa_1.45.1.tgz(r-4.6-x86_64)msa_1.45.1.tgz(r-4.6-arm64)msa_1.45.1.tgz(r-4.5-x86_64)msa_1.45.1.tgz(r-4.5-arm64)
msa_1.45.1.tar.gz(r-4.7-arm64)msa_1.45.1.tar.gz(r-4.7-x86_64)msa_1.45.1.tar.gz(r-4.6-arm64)msa_1.45.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
msa/json (API)

# 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-1.45.1(bioc 3.24)msa-1.44.0(bioc 3.23)

multiplesequencealignment alignment multiplecomparison sequencing cpp

11.58 score 25 stars 8 packages 1.3k scripts 50 mentions 13 exports 10 dependencies

Last updated from:13ac2416f3. Checks:12 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	365
linux-devel-arm64	WARNING	318
linux-devel-x86_64	WARNING	439
source / vignettes	OK	518
linux-release-arm64	WARNING	341
linux-release-x86_64	WARNING	405
macos-release-arm64	WARNING	401
macos-release-x86_64	WARNING	1242
macos-oldrel-arm64	WARNING	234
macos-oldrel-x86_64	WARNING	694
windows-devel	WARNING	523
windows-release	WARNING	565
windows-oldrel	WARNING	457
wasm-release	FAIL	214

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

Dependencies:BiocGenerics Biostrings crayon generics IRanges MultipleAlignment Rcpp S4Vectors Seqinfo XVector

msa - An R Package for Multiple Sequence Alignment

Rendered frommsa.Rnwusingknitr::knitr

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