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
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rMSA.pdf |rMSA.html✨
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:

bioinformatics sequence-alignment

27 exports 9 stars 1.16 score 26 dependencies

Last updated 2 months agofrom:4772797ab6

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 askpass BiocGenerics Biostrings crayon curl digest GenomeInfoDb GenomeInfoDbData httr IRanges jsonlite lattice mime nlme openssl proxy pwalign R6 Rcpp S4Vectors seqLogo sys UCSC.utils XVector zlibbioc

Interface to Popular Multiple Sequence Alignment Tools

Rendered fromrMSA.Rnwusingutils::Sweaveon Jul 21 2024.

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