MAFFT Alignment

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Description

Align a set of sequences using the MAFFT executable.

Usage

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mafft(x, run.label = "align.mafft", delete.output = TRUE, op = 3,
  ep = 0.123, maxiterate = 0, quiet = FALSE, num.cores = 1,
  opts = "--auto")

Arguments

x

a list or a matrix of DNA sequences (see write.dna).

run.label

label for output alignment FASTA file.

delete.output

logical. Delete output alignment FASTA file?

op

gap opening penalty.

ep

offset value, which works like gap extension penalty.

maxiterate

number cycles of iterative refinement are performed.

quiet

logical. Run MAFFT quietly?

num.cores

number of cores to be used. Passed to MAFFT argument --thread.

opts

character string other options to provide to command line.

Value

a DNAbin object with aligned sequences.

Note

MAFFT is not included with strataG and must be downloaded separately. Additionally, it must be installed such that it can be run from the command line in the current working directory. See the vignette for external.programs for installation instructions.

Author(s)

Eric Archer eric.archer@noaa.gov

References

Katoh, M., Kumar, M. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066.
Available at: http://mafft.cbrc.jp/alignment/software

Examples

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## Not run: 
data(dolph.seqs)
dolph.aln <- mafft(dolph.seqs, op = 3, ep = 2)
dolph.aln

## End(Not run)

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