mafft: Align with MAFFT aligner

In iferres/phylen: Search Core Genes Using HMMs, Compute Multiple Alignment, Concatenate And Compute Phylogeny

Description

A wrapper function to run MAFFT.

Usage

mafft(infile, outfile, n_threads = 1L, type = "nuc", mode = "linsi")

Arguments

infile	character() The path to the infile.
outfile	character() The outfile name. If missing, the extension is changed to '.ali'.
n_threads	integer() The number of cpus to use.
type	One of "nuc" or "amino".
mode	Accuracy. One of "mafft", "ginsi", "linsi" or "einsi". The first one is the default MAFFT mode, very fast. The second uses mafft options "–maxiterate 1000 –globalpair". The third uses "–maxiterate 1000 –localpair" (DEFAULT). The fourth uses "–ep 0 –maxiterate 1000 –genafpair". See MAFFT manual for more details.

Value

The alignment file and the name of the outfile in the R console.

iferres/phylen documentation built on May 24, 2019, 2:04 a.m.