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This site has been replaced by the new QIIME 2 “amplicon distribution” documentation, as of the 2025.4 release of QIIME 2.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 Content on this site is no longer updated and may be out of date.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… 👴👵
mafft-add: Add sequences to multiple sequence alignment with MAFFT.¶
| Citations |
|
|---|
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 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]
--p-addfragments / --p-no-addfragments
Optimize for the addition of short sequence
fragments (for example, primer or amplicon
sequences). If not set, default sequence addition is
used. [default: False]
--p-keeplength / --p-no-keeplength
If selected, the alignment length will be
unchanged. Any added sequence that would otherwise
introduce new insertions into the alignment, will
have those insertions deleted, to preserve original
alignment length. [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).
--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_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 : 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
addfragments : Bool, optional
Optimize for the addition of short sequence fragments (for example,
primer or amplicon sequences). If not set, default sequence addition is
used.
keeplength : Bool, optional
If selected, the alignment length will be unchanged. Any added sequence
that would otherwise introduce new insertions into the alignment, will
have those insertions deleted, to preserve original alignment length.
Returns
-------
expanded_alignment : FeatureData[AlignedSequence]
Alignment containing the provided aligned and unaligned sequences.