Muscle3App

class biotite.application_v2.muscle.Muscle3App(path: PathLike[str] | str = 'muscle')

Bases: LocalApp

A handle to MUSCLE version 3.

Parameters:

pathstr, optional

Path of the MUSCLE binary.

See also

Muscle5App

Interface to MUSCLE version >=5.

Examples

>>> sequences = [
...     ProteinSequence("BIQTITE"),
...     ProteinSequence("TITANITE"),
...     ProteinSequence("BISMITE"),
...     ProteinSequence("IQLITE"),
... ]
>>> result = Muscle3App().run(sequences).result()
>>> print(result.alignment)
BIQT-ITE
TITANITE
BISM-ITE
-IQL-ITE

run(sequences: Sequence[Sequence], matrix: SubstitutionMatrix | None = None, gap_penalty: float | tuple[float, float] | None = None, **kwargs: Any) → CommandSetup[Muscle3Result]

Perform a multiple sequence alignment.

Parameters:

sequencesiterable object of Sequence

The sequences to be aligned.

matrixSubstitutionMatrix, optional

A custom substitution matrix.

gap_penaltyfloat or tuple of (float, float), optional

If a float is provided, the value will be interpreted as general gap penalty. If a tuple is provided, an affine gap penalty is used. The first value in the tuple is the gap opening penalty, the second value is the gap extension penalty. The values need to be negative.

**kwargs

Additional command line options.

Returns:

futureFuture of Muscle3Result

A handle to the running alignment. Call Future.result() to obtain the Muscle3Result.

Gallery

Homology search and multiple sequence alignment

Homology search and multiple sequence alignment