Applications/Mafft

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

• https://mafft.cbrc.jp/alignment/software/
• https://en.wikipedia.org/wiki/MAFFT

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