Applications/Mafft

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Application Details

  • Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
  • Version: 2.2.9 (compiled with gcc)
  • Modules: bowtie2/gcc/2.2.9
  • 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


Further Information


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