seqmagick: Sequence Manipulation Utilities

Tools for reading and writing biological sequences in multiple formats, including 'FASTA', 'PHYLIP', 'CLUSTAL', 'STOCKHOLM', 'MEGA' and 'GenBank'. Supports interleaved and sequential layouts where applicable, and reads or writes gzip, bzip2 and xz compressed files transparently. Converts between formats, renames sequences via a two-column mapping, summarizes sequence counts, lengths, GC content and ambiguous characters, and manipulates sequence sets (e.g., filtering by patterns and computing consensus sequences from alignments). Also includes functions to download nucleotide records from NCBI by accession.

Version:	0.1.9
Depends:	R (≥ 4.1.0)
Imports:	Biostrings, stats, utils, yulab.utils (≥ 0.2.5)
Suggests:	knitr, rmarkdown, testthat (≥ 3.0.0), GenomicAlignments, GenomicRanges, IRanges, muscle, Rsamtools, prettydoc
Published:	2026-08-30
DOI:	10.32614/CRAN.package.seqmagick
Author:	Guangchuang Yu [aut, cre]
Maintainer:	Guangchuang Yu <guangchuangyu at gmail.com>
BugReports:	https://github.com/YuLab-SMU/seqmagick/issues
License:	Artistic-2.0
URL:	https://github.com/YuLab-SMU/seqmagick
NeedsCompilation:	no
Materials:	README, NEWS
CRAN checks:	seqmagick results

Documentation:

Reference manual:	seqmagick.html , seqmagick.pdf
Vignettes:	seqmagick introduction (source, R code)

Downloads:

Package source:	seqmagick_0.1.9.tar.gz
Windows binaries:	r-devel: seqmagick_0.1.9.zip, r-release: seqmagick_0.1.9.zip, r-oldrel: seqmagick_0.1.9.zip
macOS binaries:	r-release (arm64): seqmagick_0.1.9.tgz, r-oldrel (arm64): seqmagick_0.1.9.tgz, r-release (x86_64): seqmagick_0.1.9.tgz, r-oldrel (x86_64): seqmagick_0.1.9.tgz
Old sources:	seqmagick archive

Reverse dependencies:

Reverse imports:	ggmsa
Reverse suggests:	MicrobiotaProcess

Linking:

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