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.
