msa
Bioc currentMultiple Sequence Alignment
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
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.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
4645 7 exported
Complexity
12 avg / 103 max
Call network
4645 nodes / 6459 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
230,986
Files
924
Compiled share
96.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
7
Internal functions
42
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
42.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.3.0
System requirements
1 externalGNU make
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
23
First release
2015-09-29
Latest release
2026-08-12
Avg cadence
183 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12includes a package overview page
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 87%
- Return-value docs
- 100%
- Help pages citing references
- 100%
- fix of ClustalOmega source file squid/hsregex.c to maintain compatibility with newer versions of clang (thanks for GitHub user jeroen)
From inst/NEWS in the release
Repository practices
Checks run against github.com/ubod/msa on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| msaClustalOmegaHelp | – | – | – |
| msaClustalWHelp | – | – | – |
| msaCommonHelp | – | – | – |
| msaHelpPrefix | – | – | – |
| msaMuscleHelp | – | – | – |
Topics
Depended on by (6)
Suggested by (5)
People
- Ulrich Bodenhofer author maintainer thesis advisor
- Enrico Bonatesta author
- Christoph Kainrath author
Cite
Cite this package
Run in R for the authors' entry:
citation("msa")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btv494.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.