`ClustalOmegaApp`#

class biotite.application_v2.clustalo.ClustalOmegaApp(path: PathLike[str] | str = 'clustalo')[source]#

Bases: LocalApp

A handle to Clustal-Omega.

Parameters:

pathstr, optional: Path of the Clustal-Omega binary.

Examples

>>> sequences = [
...     ProteinSequence("BIQTITE"),
...     ProteinSequence("TITANITE"),
...     ProteinSequence("BISMITE"),
...     ProteinSequence("IQLITE"),
... ]
>>> result = ClustalOmegaApp().run(sequences).result()
>>> print(result.alignment)
-BIQTITE
TITANITE
-BISMITE
--IQLITE

run(sequences: Sequence[Sequence], distance_matrix: ndarray | None = None, guide_tree: Tree | None = None, use_full_matrix: bool = False, **kwargs: Any) → CommandSetup[ClustalOmegaResult]#

Perform a multiple sequence alignment.

Parameters:

sequencesiterable object of Sequence: The sequences to be aligned.
distance_matrixndarray, shape=(n,n), dtype=float, optional: Pairwise sequence distances used to calculate the guide tree.
guide_treeTree, optional: The guide tree used for the progressive alignment.
use_full_matrixbool, optional: If set, the full distance matrix is used for the guide-tree calculation, equivalent to the --full option, instead of the default mBed heuristic. This is required to obtain the distance matrix in the result.
**kwargs: Additional command line options.

Returns: