mkt.databases.aligners.ClustalOmegaAligner

class mkt.databases.aligners.ClustalOmegaAligner(list_sequences: list[str], substitution_matrix: str = 'BLOSUM62', path_bin: str = '/usr/local/bin/clustalo')

Bases: CustomAligner

ClustalOmega aligner class for multiple sequence alignments (need to initialize with list of sequences).

__init__(list_sequences: list[str], substitution_matrix: str = 'BLOSUM62', path_bin: str = '/usr/local/bin/clustalo') → None

Methods

__eq__(other)	Return self==value.
__init__(list_sequences[, ...])
__post_init__()
align()	Abstract method for aligning sequences.

Attributes

__dataclass_fields__
__dataclass_params__
__match_args__
path_bin	Path to clustalo binary.
substitution_matrix	Substitution matrix used.
list_sequences	List of sequences to align.

__init__(list_sequences: list[str], substitution_matrix: str = 'BLOSUM62', path_bin: str = '/usr/local/bin/clustalo') → None

align() → str

Abstract method for aligning sequences.

list_sequences: list[str]

List of sequences to align.

Type:

list[str]

path_bin: str = '/usr/local/bin/clustalo'

Path to clustalo binary. Default is “/usr/local/bin/clustalo”.

Type:

str

substitution_matrix: str = 'BLOSUM62'

Substitution matrix used. Default is BLOSUM62.

Type:

str