MultiSequenceAligner

class MultiSequenceAligner(name=None, method='clustalw2', bin_fp=None)[source]

An aligner class to perform MSA.

Constructor for MultiSequenceAligner.

Parameters

  • name (Optional[str]) – Name of the aligner instance.

  • method (str) – Alignment method that will be used. Default is “clustalw2”, for other aligners refer to defined aligners. # TODO: Make a page that list currently defined aligners

  • bin_fp (Optional[str]) – Path to the aligner executable or None to use default.

Attributes

aligner

The name of the active aligner.

bin_filepath

Path to aligner executable command.

last_alignment

Last alignment results.

last_std_error

Last std-error.

last_std_out

Last std-out.

name

Name/label of the instance.

Methods

align(input, **kwargs)

Perform MSA alignment.