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MUSCLE (BioConductor)

MUSCLE (BioConductor)

An R package of multiple sequence alignment with MUSCLE.

Topic

Genomics; Sequencing; Sequence analysis

Details

  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: FASTA; CLUSTALW; HTML; PHYLIP; MSF
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: Not stated
  • Cost: -
  • Version name: 3.26.0
  • Maturity: Mature
  • Credit: -
  • Contact: alex.t.kalinka _at_ gmail.com
  • Collection: BioConductor

Publications

Edgar RC "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic Acids Res. 2004 ;32(5) https://doi.org/10.1093/nar/gkh340
PMID: 15034147
PMCID: PMC390337


Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590


Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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