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midpoint-root: Midpoint root an unrooted phylogenetic tree.¶
Docstring:
Usage: qiime phylogeny midpoint-root [OPTIONS]
Midpoint root an unrooted phylogenetic tree.
Inputs:
--i-tree ARTIFACT The phylogenetic tree to be rooted.
Phylogeny[Unrooted] [required]
Outputs:
--o-rooted-tree ARTIFACT
Phylogeny[Rooted] The rooted phylogenetic tree. [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.phylogeny.methods import midpoint_root
Docstring:
Midpoint root an unrooted phylogenetic tree.
Midpoint root an unrooted phylogenetic tree.
Parameters
----------
tree : Phylogeny[Unrooted]
The phylogenetic tree to be rooted.
Returns
-------
rooted_tree : Phylogeny[Rooted]
The rooted phylogenetic tree.