README.md
In DomBennett/om..mafft: MAFFT
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.
Install and look up help
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')
Aligning DNA sequences
Small alignment example using the --auto argument.
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 fSTEP 2 / 12 fSTEP 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 fSTEP 2 / 12 fSTEP 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.
Key arguments
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.
Links
Find out more by visiting the MAFFT
homepage.
Please cite/read
- 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
An outsider module
Learn more at outsider
website. Want to build your
own module? Check out outsider.devtools
website.
DomBennett/om..mafft documentation built on Jan. 21, 2020, 8:38 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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.
Install and look up help
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')
Aligning DNA sequences
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 fSTEP 2 / 12 fSTEP 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 fSTEP 2 / 12 fSTEP 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.
Key arguments
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.
Links
Find out more by visiting the MAFFT homepage.
Please cite/read
- 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
An outsider module
Learn more at outsider
website. Want to build your
own module? Check out outsider.devtools
website.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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