Run mafft through outsider in R
MAFFT (Multiple Alignment through Fast Fourier Transformation): Multiple alignment program for amino acid or nucleotide sequences offering range of methods: L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
library(outsider)
#> ----------------
#> outsider v 0.1.0
#> ----------------
#> - Security notice: be sure of which modules you install
module_install(repo = 'dombennett/om..mafft')
#> -----------------------------------------------------
#> Warning: You are about to install an outsider module!
#> -----------------------------------------------------
#> Outsider modules install and run external programs
#> via Docker <https://www.docker.com>. These external
#> programs may communicate with the internet and could
#> potentially be malicious.
#>
#> Be sure to know the module you are about to install:
#> Is it from a trusted developer? Are colleagues using
#> it? Is it supposed to download lots of data? Is it
#> well used (e.g. check number of stars on GitHub)?
#> -----------------------------------------------------
#> Module information
#> -----------------------------------------------------
#> program: mafft
#> details: Multiple alignment program for amino acid or nucleotide sequences
#> docker: dombennett
#> github: dombennett
#> url: https://github.com/DomBennett/om..mafft
#> image: dombennett/om_mafft
#> container: om_mafft
#> package: om..mafft
#> Travis CI: Failing/Erroring
#> -----------------------------------------------------
#> Enter any key to continue or press Esc to quit
# module_help(repo = 'dombennett/om..mafft')Small alignment example using the
--autoargument.
library(outsider)
mafft <- module_import(fname = 'mafft', repo = "dombennett/om..mafft")
# get help
mafft('--help')
#> ------------------------------------------------------------------------------
#> MAFFT v7.407 (2018/Jul/23)
#> https://mafft.cbrc.jp/alignment/software/
#> MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
#> ------------------------------------------------------------------------------
#> High speed:
#> % mafft in > out
#> % mafft --retree 1 in > out (fast)
#>
#> High accuracy (for <~200 sequences x <~2,000 aa/nt):
#> % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)
#> % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)
#> % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)
#>
#> If unsure which option to use:
#> % mafft --auto in > out
#>
#> --op # : Gap opening penalty, default: 1.53
#> --ep # : Offset (works like gap extension penalty), default: 0.0
#> --maxiterate # : Maximum number of iterative refinement, default: 0
#> --clustalout : Output: clustal format, default: fasta
#> --reorder : Outorder: aligned, default: input order
#> --quiet : Do not report progress
#> --thread # : Number of threads (if unsure, --thread -1)
# 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', '--quiet', seq_file, '>', al_file))
# verify
cat(paste0(readLines(al_file, n = 10), collapse = '\n'))
#> >X02729 Methanococcus vannielli. #
#> ----tatctattaccctacc----ctggggaatggcttggcttgaaacgccgatgaagga
#> cgtggtaagctgcgataagcctaggcgaggcgcaa-cagcctttgaacctaggatttccg
#> aatgggacttcctacttttgtaa--------------------tccgtaaggattggtaa
#> cgcgggggattgaagcatcttagtacccgcaggaaaagaaatca-actgaga-ttccgtt
#> agtagaggcgattgaacacggatcagggcaaactgaatcccttcg-------------gg
#> gagatgtggtgttatagggccttct------tttcgcctgttgagaaaagctgaagtt-g
#> actggaacg-tcacactatagagggtgaaagtcccgtaagcgcaatcgattcaggtt---
#> tgaagtgt-ccctgagtaccgtgcgttggatatcgcgcgggaatt-tgggaggcatcaac
#> ttccaactctaaatacgtttcaagaccgatagcgtac-tagtaccgcgagggaaagctga
# add new sequences using the --add argument
al_file2 <- file.path(wd, 'alignment2.fasta')
url <- 'https://raw.githubusercontent.com/DomBennett/om..mafft/master/test_data/extra_seqs.fasta'
extra_file <- file.path(wd, 'extra_seqs.fasta')
download.file(url = url, destfile = extra_file)
# (no "--quiet" this time)
mafft(arglist = c('--add', extra_file, '--reorder', al_file, '>', al_file2))
#> nadd = 3
#> nthread = 0
#> nthreadpair = 0
#> nthreadtb = 0
#> ppenalty_ex = 0
#> stacksize: 8192 kb
#> generating a scoring matrix for nucleotide (dist=200) ... done
#> Gap Penalty = -1.53, +0.00, +0.00
#>
#>
#>
#> Making a distance matrix ..
#>
#> There are 10 ambiguous characters.
#> 1 / 13
#> done.
#>
#> Constructing a UPGMA tree (efffree=0) ...
#> 0 / 13 10 / 13
#> done.
#>
#> Progressive alignment 1/2...
#> STEP 1 / 12 f��STEP 2 / 12 f��STEP 12 / 12 f��
#> done.
#>
#> Making a distance matrix from msa..
#> 0 / 13
#> done.
#>
#> Constructing a UPGMA tree (efffree=1) ...
#> 0 / 13 10 / 13
#> done.
#>
#> Progressive alignment 2/2...
#> STEP 1 / 12 f��STEP 2 / 12 f��STEP 12 / 12 f��
#> done.
#>
#> disttbfast (nuc) Version 7.407
#> alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
#> 0 thread(s)
#>
#>
#> Strategy:
#> FFT-NS-2 (Fast but rough)
#> Progressive method (guide trees were built 2 times.)
#>
#> If unsure which option to use, try 'mafft --auto input > output'.
#> For more information, see 'mafft --help', 'mafft --man' and the mafft page.
#>
#> The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
#> It tends to insert more gaps into gap-rich regions than previous versions.
#> To disable this change, add the --leavegappyregion option.mafft has the following signature:
mafft "--option" "input_file" > "output_file"
These arguments can be passed through R via the arglist as a character
vector as demonstrated in the example above. Note, option arguments
(--op, --ep, --maxiterate, etc.) must always precede the “input >
output” statement. Also note, --man does not via R.
Find out more by visiting the MAFFT homepage.
- Yamada, Tomii, Katoh 2016 (Bioinformatics 32:3246-3251) additional informationApplication of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees.
- Katoh, Standley 2016 (Bioinformatics 32:1933-1942) A simple method to control over-alignment in the MAFFT multiple sequence alignment program.
- Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability.
- Katoh, Frith 2012 (Bioinformatics 28:3144-3146) Adding unaligned sequences into an existing alignment using MAFFT and LAST.
- Katoh, Toh 2010 (Bioinformatics 26:1899-1900) Parallelization of the MAFFT multiple sequence alignment program.
- Katoh, Asimenos, Toh 2009 (Methods in Molecular Biology 537:39-64) Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics for DNA Sequence Analysis edited by D. Posada
- Katoh, Toh 2008 (BMC Bioinformatics 9:212) Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
- Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298) Recent developments in the MAFFT multiple sequence alignment program.
- Katoh, Toh 2007 (Bioinformatics 23:372-374) Errata PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences.
- Katoh, Kuma, Toh, Miyata 2005 (Nucleic Acids Res. 33:511-518) MAFFT version 5: improvement in accuracy of multiple sequence alignment. (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)
- Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
- Bennett et al. (2020). outsider: Install and run programs, outside of R, inside of R. Journal of Open Source Software, In review
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