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mafft-add: Add sequences to 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-add [OPTIONS]

  Add new sequences to an existing alignment with MAFFT.

Inputs:
  --i-alignment ARTIFACT FeatureData[AlignedSequence]
                          The alignment to which sequences should be added.
                                                                    [required]
  --i-sequences ARTIFACT FeatureData[Sequence]
                          The sequences to be added.                [required]
Parameters:
  --p-n-threads VALUE Int % Range(1, None) | Str % Choices('auto')
                          The number of threads. (Use `auto` 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]
Outputs:
  --o-expanded-alignment ARTIFACT FeatureData[AlignedSequence]
                          Alignment containing the provided aligned and
                          unaligned 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).
  --examples              Show usage examples and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.alignment.methods import mafft_add

Docstring:

Add sequences to multiple sequence alignment with MAFFT.

Add new sequences to an existing alignment with MAFFT.

Parameters
----------
alignment : FeatureData[AlignedSequence]
    The alignment to which sequences should be added.
sequences : FeatureData[Sequence]
    The sequences to be added.
n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
    The number of threads. (Use `auto` 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
-------
expanded_alignment : FeatureData[AlignedSequence]
    Alignment containing the provided aligned and unaligned sequences.