mafft: MAFFT Alignment

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

MAFFT Alignment

Description

Align a set of sequences using the MAFFT executable.

Usage

mafft(
  x,
  op = 3,
  ep = 0.123,
  maxiterate = 0,
  quiet = TRUE,
  num.cores = 1,
  opts = "--auto",
  simplify = TRUE
)

Arguments

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

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 [e-mail]

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

## End(Not run)

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.