mafft: Multiple Alignment through Fast Fourier Transformation

In DomBennett/om..mafft: MAFFT

Description

Run the muleiple alignment program mafft.

Usage

mafft(arglist = arglist_get(...))

Arguments

arglist

Arguments as character vector passed to mafft

Examples

library(outsider)

# import
mafft <- module_import('mafft', repo = 'dombennett/om..mafft')

# get help
mafft('--help')

# download
wd <- file.path(tempdir(), 'mafft_example')
if (!dir.exists(wd)) {
  dir.create(wd)
}
# example DNA
seq_file <- file.path(wd, 'example_seq.fasta')
url <- 'https://raw.githubusercontent.com/DomBennett/om..pasta/master/example_seq.fasta'
download.file(url = url, destfile = seq_file)

# align
al_file <- file.path(wd, 'alignment.fasta')
mafft(arglist = c('--auto', seq_file, '>', al_file))

DomBennett/om..mafft documentation built on Jan. 21, 2020, 8:38 p.m.