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mafft: De novo multiple sequence alignment with MAFFT

Citations

[alignment:mafft:KS13]Kazutaka Katoh and Daron M Standley. Mafft multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4):772–780, 2013. doi:10.1093/molbev/mst010.

Docstring:

Usage: qiime alignment mafft [OPTIONS]

  Perform de novo multiple sequence alignment using MAFFT.

Options:
  --i-sequences ARTIFACT PATH FeatureData[Sequence]
                                  The sequences to be aligned.  [required]
  --p-n-threads INTEGER RANGE     The number of threads. (Use 0 to
                                  automatically use all available cores)
                                  [default: 1]
  --p-parttree / --p-no-parttree  This flag is required if the number of
                                  sequences being aligned are larger than
                                  1000000. Disabled by default  [default:
                                  False]
  --o-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  The aligned sequences.  [required if not
                                  passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.alignment.methods import mafft

Docstring:

De novo multiple sequence alignment with MAFFT

Perform de novo multiple sequence alignment using MAFFT.

Parameters
----------
sequences : FeatureData[Sequence]
    The sequences to be aligned.
n_threads : Int % Range(0, None), optional
    The number of threads. (Use 0 to automatically use all available cores)
parttree : Bool, optional
    This flag is required if the number of sequences being aligned are
    larger than 1000000. Disabled by default

Returns
-------
alignment : FeatureData[AlignedSequence]
    The aligned sequences.