Muscle5App

class biotite.application_v2.muscle.Muscle5App(path: PathLike[str] | str = 'muscle')

Bases: LocalApp

A handle to MUSCLE version 5.

Parameters:

pathstr, optional

Path of the MUSCLE binary.

See also

Muscle3App

Interface to MUSCLE version <5.

Notes

Alignment ensemble generation is not supported, yet.

Examples

>>> sequences = [
...     ProteinSequence("BIQTITE"),
...     ProteinSequence("TITANITE"),
...     ProteinSequence("BISMITE"),
...     ProteinSequence("IQLITE"),
... ]
>>> result = Muscle5App().run(sequences).result()
>>> print(result.alignment)
BI-QTITE
TITANITE
BI-SMITE
-I-QLITE

run(sequences: Sequence[Sequence], super5: bool = False, **kwargs: Any) → CommandSetup[Muscle5Result]

Perform a multiple sequence alignment.

Parameters:

sequencesiterable object of Sequence

The sequences to be aligned.

super5bool, optional

If set, the Super5 algorithm is used for the alignment, which is faster for a large number of sequences.

**kwargs

Additional command line options.

Returns:

futureFuture of Muscle5Result

A handle to the running alignment. Call Future.result() to obtain the Muscle5Result.