Difference between revisions of "Applications/Mafft"

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==Application Details==
 
==Application Details==
  
* Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.  
+
* Description: MAFFT is used to create multiple sequence alignments of amino acid or nucleotide sequences.
 
* Version: 2.2.9 (compiled with gcc)
 
* Version: 2.2.9 (compiled with gcc)
* Modules: bowtie2/gcc/2.2.9
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* Modules: mafft/7.397
* Licence: Open source (Github)  
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* Licence: Open source (Github)
  
 
==Usage Examples==
 
==Usage Examples==
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[username@login01 ~]$ mafft --auto input > output
 
[username@login01 ~]$ mafft --auto input > output
 
</pre>
 
</pre>
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 +
===Batch Job===
 +
<!-- ty NIH: https://hpc.nih.gov/apps/mafft.html -->
 +
<pre>
 +
#!/bin/bash
 +
#SBATCH J mafftjob
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#SBATCH N 1
 +
#SBATCH --exclusive
 +
#SBATCH --cpus-per-task=4
 +
#SBATCH -o %N-%j.out
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#SBATCH -e %N-%j.err
 +
 
 +
module purge
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module load mafft/7.397
 +
 
 +
mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile
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</pre>
  
 
==Further Information==
 
==Further Information==
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* [https://mafft.cbrc.jp/alignment/software/ https://mafft.cbrc.jp/alignment/software/]
 
* [https://mafft.cbrc.jp/alignment/software/ https://mafft.cbrc.jp/alignment/software/]
 
* [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT]
 
* [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT]
 
  
 
{{Modulepagenav}}
 
{{Modulepagenav}}

Latest revision as of 12:54, 17 November 2022

Application Details

  • Description: MAFFT is used to create multiple sequence alignments of amino acid or nucleotide sequences.
  • Version: 2.2.9 (compiled with gcc)
  • Modules: mafft/7.397
  • Licence: Open source (Github)

Usage Examples

Manual execution

[username@login01 ~]$ module add mafft/7.397
[username@login01 ~]$ mafft

---------------------------------------------------------------------

   MAFFT v7.397 (2018/Apr/16)

        MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
        https://mafft.cbrc.jp/alignment/software/
---------------------------------------------------------------------


Input file? (fasta format)
@


Command line processing

[username@login01 ~]$ module add mafft/7.397
[username@login01 ~]$ mafft [arguments] input > output


An alias for an accurate option (L-INS-i) for an alignment of up to ∼200 sequences × ∼2,000 sites:

[username@login01 ~]$ mafft-linsi input > output


A fast option (FFT-NS-2) for a larger sequence alignment:

[username@login01 ~]$ mafft input > output


If not sure which option to use,

[username@login01 ~]$ mafft --auto input > output

Batch Job

#!/bin/bash
#SBATCH J mafftjob
#SBATCH N 1
#SBATCH --exclusive
#SBATCH --cpus-per-task=4
#SBATCH -o %N-%j.out
#SBATCH -e %N-%j.err

module purge
module load mafft/7.397

mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile

Further Information





Modules | Main Page | Further Topics