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mafft: De novo multiple sequence alignment with MAFFT

Citations
  • 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.

Inputs:
  --i-sequences ARTIFACT FeatureData[Sequence]
                          The sequences to be aligned.              [required]
Parameters:
  --p-n-threads INTEGER   The number of threads. (Use 0 to automatically use
    Range(0, None)        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]
Outputs:
  --o-alignment ARTIFACT FeatureData[AlignedSequence]
                          The aligned sequences.                    [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --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.