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mafft: De novo multiple sequence alignment with MAFFT¶
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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 NTHREADS 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-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). --example-data PATH Write example data and exit. --citations Show citations and exit. --use-cache DIRECTORY Specify the cache to be used for the intermediate work of this action. If not provided, the default cache under $TMP/qiime2/will be used. IMPORTANT FOR HPC USERS: If you are on an HPC system and are using parallel execution it is important to set this to a location that is globally accessible to all nodes in the cluster. --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 : Threads, 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 ------- alignment : FeatureData[AlignedSequence] The aligned sequences.