R Observatory: Metrics for muscle version 3.8.31-4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2014-07-07. Its history is shown below.

Reason: This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/muscle.html>

Details below reflect version 3.8.31-4, its last release before removal.

muscle

3.8.31-4Package record

Multiple Sequence Alignment

0packages dependsuggested by 4

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Alex T. KalinkaCRAN page ↗Website ↗

MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.

Install

BioconductorR (source archive)

BiocManager::install("muscle")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/muscle/muscle_3.8.31-4.tar.gz"
pkgFile <- "muscle_3.8.31-4.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (3.8.31-4) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.8.31-4

READMENoVignettesNoNEWSNoCitation fileYes · cites a publicationWebsiteYes

Help pages: 7includes a package overview page
Examples that run: 33%2 run in a plain check · 4 never run
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 43%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on452 r2u2.6K bioconda31 c2d4u

How downloads are counted

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Suggested by 4

Suggests, most downloaded first

seqmagick BOLDconnectR orthGS BOLDNODE

How these are counted

Code & Tests

Datasets

People & History

People (1)

Robert C. Edgar. R port by Alex T. Kalinka.

Contributor

Maintainer since 3.8.31-0 (2012)

Releases (5)

Pick two releases to compare their code metrics.

3.8.31-4archived
2014-07-07 · diff ↗
This package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/muscle.html>
R
R 3.0.0 released · 2013-04-03
3.8.31-4
record
2012-10-05 · diff ↗
3.8.31-3
record
2012-10-05 · diff ↗
3.8.31-2
record
2012-10-05 · diff ↗
3.8.31-1
record
2012-10-05 · diff ↗
3.8.31-0
record
2012-10-05
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-10-05
Total releases: 5 / 14 yrs
License: Unlimited
Bundled data: 1.7 KB / 1 file

Cite

Cite this package

Run in R for the authors' entry:

citation("muscle")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/nar/gkh340.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for muscle version 3.8.31-4 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

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.

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