index.rst

MAFFT-7.402

Basic Information

• Deploy date: 27 July 2018
• Official Website: https://mafft.cbrc.jp/alignment/software/
• License: BSD License
  • Extensions:
    • Mxcarna: BSD License (For more information check README file in mafft-7.402-with-extensions/extensions/mxscarna_src/
    • Foldalign: GNU GPL-2
    • Contrafold: BSD License
• Installed on: :ref:`Apolo II <about_apolo-ii>`, :ref:`Cronos <about_cronos>`

Installation

This entry covers the entire process performed for the installation and configuration of MAFFT with extensions (MXSCARNA, Foldalign and CONTRAfold) on a cluster.

.. toctree::
   :maxdepth: 2

   installation

Usage

This section describes the method to submit jobs with the resource manager SLURM.

1. Load the necessary environment.

   module load mafft/7.402-with-extensions_intel-X.X.X

   Note

   Remember to load the proper environment for Cronos or Apolo

   • Apolo

   • module load mafft/7.402-with-extensions_intel-17.0.1
     • Cronos
   • module load mafft/7.402-with-extensions_intel-18.0.2

2. Run MAFFT with SLURM.

   An example:

   Note

   This example was tested with :download:`example.fa <src/example.fa>` that contains unlined DNA secuences.

   .. literalinclude:: src/mafft.sh
      :language: bash
      :caption: :download:`mafft.sh <src/mafft.sh>`
   
   
   

   Options

   • quiet → Do not report progress and this flag is mandatory to run unattended jobs.
   • auto → Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size.
   • thread → Number of threads (number of cores reserved on SLURM).

   Note

   For more information, please read the manual entry for Mafft man mafft or mafft -h

Authors

• Manuela Carrasco Pinzón <mcarras1@eafit.edu.co>