Warning
This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2. You can still access the content from the “old docs” here for the QIIME 2 2024.10 and earlier releases, but we recommend that you transition to the new documentation at https://amplicon-docs.qiime2.org. Content on this site is no longer updated and may be out of date.
Are you looking for:
the QIIME 2 homepage? That’s https://qiime2.org.
learning resources for microbiome marker gene (i.e., amplicon) analysis? See the QIIME 2 amplicon distribution documentation.
learning resources for microbiome metagenome analysis? See the MOSHPIT documentation.
installation instructions, plugins, books, videos, workshops, or resources? See the QIIME 2 Library.
general help? See the QIIME 2 Forum.
Old content beyond this point… 👴👵
filter-tree: Remove features from tree based on metadata¶
Docstring:
Usage: qiime phylogeny filter-tree [OPTIONS]
Remove tips from a tree if their identifiers based on a set of provided
identifiers.
Inputs:
--i-tree ARTIFACT Phylogeny[Rooted¹ | Unrooted²]
Tree that should be filtered [required]
--i-table ARTIFACT FeatureTable[Frequency | RelativeFrequency |
PresenceAbsence | Composition]
Feature table which contains the identifier that
should be retained in the tree [optional]
Parameters:
--m-metadata-file METADATA...
(multiple Feature metadata to use with the 'where' statement
arguments will be or to select tips to be retained. Metadata objects
merged) could also include FeatureData[Sequence] data types,
if, forinstance, you want to filter to match
represenative sequencces. [optional]
--p-where TEXT SQLite WHERE clause specifying sample metadata
criteria that must be met to be included in the
filtered feature table. If not provided, all samples
in `metadata` that are also in the feature table will
be retained. [optional]
Outputs:
--o-filtered-tree ARTIFACT Phylogeny[Rooted¹ | Unrooted²]
The resulting 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 filter_tree
Docstring:
Remove features from tree based on metadata
Remove tips from a tree if their identifiers based on a set of provided
identifiers.
Parameters
----------
tree : Phylogeny[Rooted¹ | Unrooted²]
Tree that should be filtered
table : FeatureTable[Frequency | RelativeFrequency | PresenceAbsence | Composition], optional
Feature table which contains the identifier that should be retained in
the tree
metadata : Metadata, optional
Feature metadata to use with the 'where' statement or to select tips to
be retained. Metadata objects could also include FeatureData[Sequence]
data types, if, forinstance, you want to filter to match represenative
sequencces.
where : Str, optional
SQLite WHERE clause specifying sample metadata criteria that must be
met to be included in the filtered feature table. If not provided, all
samples in `metadata` that are also in the feature table will be
retained.
Returns
-------
filtered_tree : Phylogeny[Rooted¹ | Unrooted²]
The resulting phylogenetic tree.