R: Sequence Alignment with MAFFT

mafft {ips}

R Documentation

Sequence Alignment with MAFFT

Description

This function is a wrapper for MAFFT and can be used for (profile) aligning of DNA and amino acid sequences.

Usage

mafft(
  x,
  y,
  add,
  method = "auto",
  maxiterate = 0,
  op = 1.53,
  ep = 0,
  gt = NULL,
  options,
  thread = -1,
  exec,
  quiet,
  file
)

Arguments

`x`	An object of class `DNAbin` or `AAbin`.
`y`	An object of class `DNAbin` or `AAbin`, if given both `x` and `y` are preserved and aligned to each other ("profile alignment").
`add`	A character string giving the method used for adding `y` to `x`: `"add"`, `"addprofile"` (default), or any unambiguous abbreviation of these.
`method`	A character string giving the alignment method. Available accuracy-oriented methods for less than 200 sequences are `"localpair"`, `"globalpair"`, and `"genafpair"`; `"retree 1"` and `"retree 2"` are for speed-oriented alignment. The default is `"auto"`, which lets MAFFT choose an appropriate alignment method.
`maxiterate`	An integer giving the number of cycles of iterative refinement to perform. Possible choices are `0`: progressive method, no iterative refinement (default); `2`: two cycles of iterative refinement; `1000`: at most 1000 cycles of iterative refinement.
`op`	A numeric giving the `gap opening penalty` at group-to-group alignment; default 1.53.
`ep`	A numeric giving the offset value, which works like `gap extension penalty`, for group-to-group alignment; default 0.0, but 0.123 is recommended if no long indels are expected.
`gt`	An object of class `phylo` that is to be used as a guide tree during alignment. The default is to let MAFFT use its own internal guide tree
`options`	A vector of mode character specifying additional arguments to MAFFT, that are not included in `mafft` such as, e.g., `--adjustdirection`.
`thread`	Integer giving the number of physical cores MAFFT should use; with `thread = -1` the number of cores is determined automatically.
`exec`	A character string giving the path to the MAFFT executable including its name, e.g. something like `/user/local/bin/mafft` under UNIX-alikes.
`quiet`	Logical, if set to `TRUE`, mafft progress is printed out on the screen.
`file`	A character string indicating the filename of the output FASTA file; if this is missing the the alignment will be returned as matrix of class `DNAbin` or `AAbin`.

Details

"localpair" selects the L-INS-i algorithm, probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information.

"globalpair" selects the G-INS-i algorithm suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information.

"genafpair" selects the E-INS-i algorithm suitable for sequences containing large unalignable regions; recommended for <200 sequences.

"retree 1" selects the FFT-NS-1 algorithm, the simplest progressive option in MAFFT; recommended for >200 sequences.

"retree 2" selects the FFT-NS-2 algorithm that uses a second iteration of alignment based on a guide tree computed from an FFT-NS-1 alignment; this is the default in MAFFT; recommended for >200 sequences.

Value

A matrix of class "DNAbin" or "AAbin".

Note

mafft was last updated and tested to work with MAFFT 7.205. If you have problems getting the function to work with a newer version of MAFFT, please contact the package maintainer.

References

Katoh, K. and H. Toh. 2008. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286-298.

Katoh, K., K.-i. Kuma, H. Toh, and T. Miyata. 2005. Mafft version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511–518.

Katoh, K., K. Misawa, K.-i. Kuma, and T. Miyata. 2002. Mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleid Acids Research 30: 3059–3066.

https://mafft.cbrc.jp/alignment/software/index.html