mafft: DNA Sequence Alignment with MAFFT

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

The function is a wrapper to MAFFT an can be used for sequence and profile aligning.

Usage

mafft(x, y, add, method = "localpair", maxiterate = 1000, op = 1.53, 
    ep = 0.0, path, quiet)

Arguments

x	an object of class DNAbin.
y	an object of class DNAbin, 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 abbreviatin of these.
method	a character string giving the alignment method. Available accuracy-oriented methods for less than 200 sequences are "localpair", "globalpair", and "genafpair" as well as "retree 1" and "retree 2"for speed-oriented alignment.
maxiterate	an integer giving the number of cycles of iterative refinement to perform; default 1000
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
path	a character string indicating the path to the MAFFT executable.
quiet	logical: if set to TRUE, mafft progress is printed out on the screen

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 use an second iteration of alignment based on a guide tree computed from an FFT-NS-1 aligment; recommended for >200 sequences.

Value

A matrix of class "DNAbin".

Note

mafft was last updated and tested to work with MAFFT 7.032. If you have problems getting the function to work with a newer version of MAFFT, please contact the package maintainer.

Author(s)

Christoph Heibl

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.

http://align.bmr.kyushu-u.ac.jp/mafft/software/

See Also

read.fas to import DNA sequences; prank for another alignment algorithm; gblocks and aliscore for alignment cleaning.

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.