strataG (version 2.4.905)

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",
  simplify = TRUE
)

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

The number of cores to use. If set to NULL, the value will be what is reported by detectCores - 1. Passed to MAFFT argument --thread.

opts

character string other options to provide to command line.

simplify

if TRUE, if x is a single sequence, a single DNAbin object is returned, otherwise, a list of alignments is returned.

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

Examples

# NOT RUN {
data(dolph.seqs)
dolph.aln <- mafft(dolph.seqs, op = 3, ep = 2)
dolph.aln
# }
# NOT RUN {
# }