muscle

This is the released version of muscle; for the devel version, see muscle.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

Multiple Sequence Alignment with MUSCLE

Bioconductor version: Release (3.23)

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

Author: Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.

Maintainer: Alex T. Kalinka <alex.t.kalinka at gmail.com>

Citation (from within R, enter citation("muscle")):

Algorithm by Robert C. Edgar. R port by Alex T. Kalinka. muscle: Multiple Sequence Alignment with MUSCLE. doi:10.18129/B9.bioc.muscle, R package version 3.54.0, https://bioconductor.org/packages/muscle.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("muscle")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("muscle")

A guide to using muscle	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, DataImport, Genetics, MultipleSequenceAlignment, SequenceMatching, Sequencing, Software
Version	3.54.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	Unlimited
Depends	Biostrings
Imports
System Requirements
URL	http://www.drive5.com/muscle/

Suggests
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	BOLDconnectR, BOLDNODE, orthGS, seqmagick
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	muscle_3.54.0.tar.gz
Windows Binary (x86_64)	muscle_3.54.0.zip
macOS Binary (big-sur-x86_64)	muscle_3.54.0.tgz
macOS Binary (sonoma-arm64)	muscle_3.54.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/muscle
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/muscle
Package Short Url	https://bioconductor.org/packages/muscle/
Package Downloads Report	Download Stats