This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
This QIIME 2 plugin provides support for generating and manipulating sequence alignments.
- version:
2025.7.0.dev0 - website: https://
github .com /qiime2 /q2 -alignment - user support:
- Please post to the QIIME 2 forum for help with this plugin: https://
forum .qiime2 .org
Actions¶
| Name | Type | Short Description |
|---|---|---|
| mafft | method | De novo multiple sequence alignment with MAFFT |
| mafft-add | method | Add sequences to multiple sequence alignment with MAFFT. |
| mask | method | Positional conservation and gap filtering. |
alignment mafft¶
Perform de novo multiple sequence alignment using MAFFT.
Citations¶
Inputs¶
- sequences:
FeatureData[Sequence] The sequences to be aligned.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]
Outputs¶
- alignment:
FeatureData[AlignedSequence] The aligned sequences.[required]
alignment mafft-add¶
Add new sequences to an existing alignment with MAFFT.
Citations¶
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to which sequences should be added.[required]
- sequences:
FeatureData[Sequence] The sequences to be added.[required]
Parameters¶
- n_threads:
Threads The number of threads. (Use
autoto automatically use all available cores)[default:1]- parttree:
Bool This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default[default:
False]- addfragments:
Bool Optimize for the addition of short sequence fragments (for example, primer or amplicon sequences). If not set, default sequence addition is used.[default:
False]- keeplength:
Bool 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¶
- expanded_alignment:
FeatureData[AlignedSequence] Alignment containing the provided aligned and unaligned sequences.[required]
alignment mask¶
Mask (i.e., filter) unconserved and highly gapped columns from an alignment. Default min_conservation was chosen to reproduce the mask presented in Lane (1991).
Citations¶
Lane, 1991
Inputs¶
- alignment:
FeatureData[AlignedSequence] The alignment to be masked.[required]
Parameters¶
- max_gap_frequency:
Float%Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency.[default:
1.0]- min_conservation:
Float%Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences.[default:
0.4]
Outputs¶
- masked_alignment:
FeatureData[AlignedSequence] The masked alignment.[required]
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