stepMAFFT: STEP G: MAFFT Alignment

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Use MAFFT to align tip-rank-level sequences.

Usage

stepMAFFT(x, method = "auto", maxiterate = 0, op = 1.53, ep = 0)

Arguments

x	An object of class megapteraProj.
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.

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 aligment; this is the default in MAFFT; recommended for >200 sequences.

Value

None, stepMAFFT is called for its side effect.

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

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.