Package: rMSA 0.99.1

rMSA: Interface for Popular Multiple Sequence Alignment Tools

Seamlessly interfaces the Multiple Sequence Alignment software packages ClustalW, MAFFT, MUSCLE and Kalign (downloaded separately) and provides support to calcualte distances between sequences. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.

Authors:Michael Hahsler, Anurag Nagar

rMSA_0.99.1.tar.gz
rMSA_0.99.1.zip(r-4.7)rMSA_0.99.1.zip(r-4.6)rMSA_0.99.1.zip(r-4.5)
rMSA_0.99.1.tgz(r-4.6-any)rMSA_0.99.1.tgz(r-4.5-any)
rMSA_0.99.1.tar.gz(r-4.7-any)rMSA_0.99.1.tar.gz(r-4.6-any)
rMSA_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rMSA/json (API)

# Install 'rMSA' in R:

install.packages('rMSA', repos = c('https://mhahsler.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mhahsler/rmsa/issues

On CRAN:

genetics sequencing infrastructure alignment bioinformatics sequence-alignment

3.78 score 12 stars 7 scripts 27 exports 16 dependencies

Last updated from:4772797ab6. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	149
source / vignettes	OK	162
linux-release-x86_64	ERROR	150
macos-release-arm64	ERROR	149
macos-oldrel-arm64	ERROR	123
windows-devel	ERROR	112
windows-release	ERROR	119
windows-oldrel	ERROR	98
wasm-release	OK	138

Exports:boxshade boxshade_help c2s clustal clustal_help distAlignment distApe distCV distEdit distFFP distKMer distNSV distSimRank kalign kalign_help mafft mafft_help muscle muscle_help mutations plot.DNAMultipleAlignment plot.DNAStringSet plot.RNAMultipleAlignment plot.RNAStringSet random_sequences s2c simRank

Dependencies:ape BiocGenerics Biostrings crayon digest generics IRanges lattice nlme proxy pwalign Rcpp S4Vectors Seqinfo seqLogo XVector

Rendered fromrMSA.Rnwusingutils::Sweave

Last update: 2015-10-06
Started: 2015-10-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Boxshade: Shading Multiple Aligned Sequences	box boxshade boxshade_help
Run Multiple Sequence Alignment (ClustalW) on a Set of Sequences	clustal clustal_help
Calculate Distances between Sets of Sequences	dist distAlignment distApe distCV distEdit distFFP distKMer distNSV distSimRank
Multiple Sequence Alignment (Kalign)	kalign kalign_help
Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences	mafft mafft_help
Run Multiple Sequence Alignment (MUSCLE) on a Set of Sequences	muscle muscle_help
Creates Random Mutations of a Sequence	mutations
Plot Genetic Sequences and Alignments	plot plot.DNAMultipleAlignment plot.DNAStringSet plot.RNAMultipleAlignment plot.RNAStringSet
Create a Set of Random Sequences	random_sequences
Compute the SimRank Similarity between Sets of Sequences	simRank
Convenience Functions to Convert Strings to Character Vectors	c2s s2c