Package: msa 1.39.0
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:
msa_1.39.0.tar.gz
msa_1.39.0.zip(r-4.5)msa_1.39.0.zip(r-4.4)msa_1.39.0.zip(r-4.3)
msa_1.39.0.tgz(r-4.4-x86_64)msa_1.39.0.tgz(r-4.4-arm64)msa_1.39.0.tgz(r-4.3-x86_64)msa_1.39.0.tgz(r-4.3-arm64)
msa_1.39.0.tar.gz(r-4.5-noble)msa_1.39.0.tar.gz(r-4.4-noble)
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
On BioConductor:msa-1.39.0(bioc 3.21)msa-1.38.0(bioc 3.20)
multiplesequencealignmentalignmentmultiplecomparisonsequencingcpp
Last updated 2 months agofrom:76c1c299fd. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 03 2024 |
| R-4.5-win-x86_64 | WARNING | Dec 03 2024 |
| R-4.5-linux-x86_64 | WARNING | Dec 03 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 03 2024 |
| R-4.4-mac-x86_64 | WARNING | Dec 03 2024 |
| R-4.4-mac-aarch64 | WARNING | Dec 03 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 03 2024 |
| R-4.3-mac-x86_64 | WARNING | Dec 03 2024 |
| R-4.3-mac-aarch64 | WARNING | Dec 03 2024 |
Exports:msamsaCheckNamesmsaClustalOmegamsaClustalWmsaConsensusSequencemsaConservationScoremsaConvertmsaMusclemsaPrettyPrintparamsprintshowversion
Dependencies:askpassBiocGenericsBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitemimeopensslR6RcppS4VectorssysUCSC.utilsXVectorzlibbioc
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 |
