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msa

R package for multiple sequence alignment

https://github.com/ubod/msa

Science Score: 39.0%

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    Found 18 DOI reference(s) in README
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Last synced: 10 months ago · JSON representation

Repository

R package for multiple sequence alignment

Basic Info
Statistics
  • Stars: 19
  • Watchers: 1
  • Forks: 13
  • Open Issues: 1
  • Releases: 0
Created about 8 years ago · Last pushed 10 months ago
Metadata Files
Readme

README.md

msa: An R Package for 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.

Although the package is maintained by Ulrich Bodenhofer, the package itself has been implemented mainly by Enrico Bonatesta and Christoph Kainrath (formerly Christoph Horejs-Kainrath).

Installation

The package can be installed from Bioconductor. Therefore, the the simplest way to install the package is to enter ``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("msa") ``` into your R session. If, for what reason ever, you prefer to install the package manually, follow the instructions in the user manual.

User support

If you encounter any issues or if you have any question that might be of interest also for other users, before writing a private message to the package developers/maintainers, please create an issue in this repository and also consider posting on Bioconductor Support or on StackOverflow. For other matters regarding the package, please contact the package author.

Citing this package

If you use this package for research that is published later, you are kindly asked to cite it as follows:

  • U. Bodenhofer, E. Bonatesta, C. Horejs-Kainrath, and S. Hochreiter (2015). msa: an R package for multiple sequence alignment. Bioinformatics 31(24):3997-3999. DOI: 10.1093/bioinformatics/btv494.

Moreover, we insist that, any time you use/cite the package, you also cite the original paper in which the algorithm/method/package that you have been using has been introduced:

ClustalW:

  • J. D. Thompson, D. G. Higgins, and T. J. Gibson (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673 4680. DOI: 10.1093/nar/22.22.4673.

ClustalOmega:

  • F. Sievers, A. Wilm, D. Dineen, T. J. Gibson, K. Karplus, W. Li, R. Lopez, H. McWilliam, M. Remmert, J. Söding, J. D. Thompson, and D. G. Higgins (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7:539. DOI: 10.1038/msb.2011.75.

MUSCLE:

  • R. C. Edgar (2004). MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(5):113. DOI: 10.1186/1471-2105-5-113.
  • R. C. Edgar (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792 1797. DOI: 10.1093/nar/gkh340.

TeXshade:

  • E. Beitz (2000). TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e. Bioinformatics 16(2):135-139. DOI: 10.1093/bioinformatics/16.2.135.

Owner

  • Login: UBod
  • Kind: user
  • Location: Hagenberg, Austria

Professor for Artificial Intelligence at University of Applied Sciences Upper Austria / Chief Artificial Intelligence Officer at QUOMATIC.AI

GitHub Events

Total
  • Issues event: 11
  • Watch event: 2
  • Issue comment event: 16
  • Push event: 10
  • Pull request event: 3
  • Fork event: 2
Last Year
  • Issues event: 11
  • Watch event: 2
  • Issue comment event: 16
  • Push event: 10
  • Pull request event: 3
  • Fork event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 34
  • Total pull requests: 8
  • Average time to close issues: 4 months
  • Average time to close pull requests: 28 days
  • Total issue authors: 28
  • Total pull request authors: 6
  • Average comments per issue: 3.18
  • Average comments per pull request: 1.88
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 7
  • Pull requests: 4
  • Average time to close issues: 6 days
  • Average time to close pull requests: about 1 month
  • Issue authors: 6
  • Pull request authors: 2
  • Average comments per issue: 1.43
  • Average comments per pull request: 0.5
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • richelbilderbeek (4)
  • francoiskroll (2)
  • msubirana (2)
  • rualmey (2)
  • BC19RG (1)
  • moa4020 (1)
  • vladimirsouza (1)
  • zhuldyzhanzak (1)
  • Yikun (1)
  • SevanEsaian (1)
  • zachpwakefield (1)
  • GeroKn (1)
  • padpadpadpad (1)
  • nick-youngblut (1)
  • JAMKuttan (1)
Pull Request Authors
  • rualmey (2)
  • Rong-Zh (2)
  • fizwit (1)
  • mephistopheles78 (1)
  • Yikun (1)
  • gancho-ivanov (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 228,467 total
  • Total dependent packages: 4
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: msa

Multiple Sequence Alignment

  • Versions: 6
  • Dependent Packages: 4
  • Dependent Repositories: 0
  • Downloads: 228,467 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 2.8%
Downloads: 8.5%
Maintainers (1)
ulrich@bodenhofer.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • Biostrings >= 2.40.0 depends
  • R >= 3.3.0 depends
  • methods * depends
  • BiocGenerics * imports
  • IRanges >= 1.20.0 imports
  • Rcpp >= 0.11.1 imports
  • S4Vectors * imports
  • tools * imports
  • Biobase * suggests
  • ape >= 5.1 suggests
  • knitr * suggests
  • phangorn * suggests
  • seqinr * suggests