Learn R Programming
strataG (version 1.0.3)

mafft: MAFFT Alignment

Description

Align a set of sequences using the MAFFT executable.

Usage

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.

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