Difference between revisions of "Applications/Mafft"
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==Application Details== | ==Application Details== | ||
| − | * Description: | + | * 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: | + | * Modules: mafft/7.397 |
| − | * Licence: Open source (Github) | + | * Licence: Open source (Github) |
==Usage Examples== | ==Usage Examples== | ||
| Line 13: | Line 13: | ||
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module | + | [username@login01 ~]$ module add mafft/7.397 |
[username@login01 ~]$ mafft | [username@login01 ~]$ mafft | ||
| Line 35: | Line 35: | ||
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module | + | [username@login01 ~]$ module add mafft/7.397 |
[username@login01 ~]$ mafft [arguments] input > output | [username@login01 ~]$ mafft [arguments] input > output | ||
</pre> | </pre> | ||
| Line 59: | Line 59: | ||
[username@login01 ~]$ mafft --auto input > output | [username@login01 ~]$ mafft --auto input > output | ||
</pre> | </pre> | ||
| − | + | ||
| + | ===Batch Job=== | ||
| + | <!-- ty NIH: https://hpc.nih.gov/apps/mafft.html --> | ||
| + | <pre> | ||
| + | #!/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 $SLURM_CPUS_PER_TASK ex1 > outfile | ||
| + | </pre> | ||
==Further Information== | ==Further Information== | ||
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* [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT] | * [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT] | ||
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Latest revision as of 12:54, 17 November 2022
Contents
Application Details
- Description: MAFFT is used to create multiple sequence alignments of amino acid or nucleotide sequences.
- Version: 2.2.9 (compiled with gcc)
- Modules: mafft/7.397
- Licence: Open source (Github)
Usage Examples
Manual execution
[username@login01 ~]$ 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