Package muscle. R topics documented: March 7, Type Package
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1 Type Package Package muscle March 7, 2019 Title Multiple Sequence Alignment with MUSCLE Version Date Author Algorithm by Robert C. Edgar. R port by Alex T. Kalinka. Maintainer Alex T. Kalinka <alex.t.kalinka@gmail.com> MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences. biocviews MultipleSequenceAlignment, Alignment, Sequencing, Genetics, SequenceMatching, DataImport Depends Biostrings License Unlimited URL LazyLoad yes LazyData yes NeedsCompilation yes git_url git_branch RELEASE_3_8 git_last_commit da46a28 git_last_commit_date Date/Publication R topics documented: muscle-package muscle Index 5 1
2 2 muscle muscle-package Multiple Sequence Alignment Details MUSCLE performs multiple sequence alignments of nucleotide and amino acid sequences. Details about the algorithm can be found on the MUSCLE website: Author(s) Algorithm: Robert C. Edgar R port: Alex T. Kalinka <alex.t.kalinka@gmail.com> Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, See Also muscle, Examples ## Align sequences in an XStringSet object. ## Not run: aln <- muscle(stringset = ) ## End(Not run) muscle Multiple Sequence Alignment Usage MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences. muscle(stringset, quiet = FALSE,...) Arguments stringset quiet An object of class XStringSet: DNAStringSet, RNAStringSet, or AAStringSet. Logical, whether to prevent printing of the progress of the algorithm to the screen. Defaults to FALSE.... Arguments (options and flags) for the MUSCLE algorithm (see Details).
3 3 Details Arguments for the MUSCLE algorithm are either options or flags. Options take a variety of values, but flags are always logicals (TRUE or FALSE). All options and flags are explained in detail on the MUSCLE website: Value Output is an object of class MultipleAlignment: DNAMultipleAlignment, RNAMultipleAlignment, or AAMultipleAlignment. Note For further details see the MUSCLE website: Author(s) Algorithm by Robert C. Edgar. Ported into R by Alex T. Kalinka <alex.t.kalinka@gmail.com> Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, See Also Examples ## Align sequences in an XStringSet object. aln <- muscle(stringset = ) ## Switch on the diags flag. aln <- muscle(stringset =, diags = TRUE) Unaligned MAX sequences Unaligned DNA sequences of the MAX gene for 31 mammalian species. Usage Format An object of class DNAStringSet.
4 4 Value Source An object of class DNAStringSet. Wagner, AJ et al. (1992) Expression, regulation, and chromosomal localization of the Max gene. Proc Natl Acad Sci USA 89:
5 Index Topic datasets, 3 AAMultipleAlignment, 3 AAStringSet, 2 DNAMultipleAlignment, 3 DNAStringSet, 2 4 MultipleAlignment, 3 muscle, 2, 2 muscle-package, 2 RNAMultipleAlignment, 3 RNAStringSet, 2, 2, 3, 3 XStringSet, 2 5
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