schrodinger.application.msv.jobs.muscle module

schrodinger.application.msv.jobs.muscle.getMusclePath()

Returns the path to the MUSCLE executable.

Return type:str Returns:path to MUSCLE executable file, or None if the executable could not be located.

schrodinger.application.msv.jobs.muscle.runMuscleAlignment(aln, second_aln=None, quiet=True, maintain_order=True)

Runs alignment via MUSCLE program

Note:

Muscle by default rearranges the order to put similar sequences together

Parameters:

• aln (ProteinAlignment) – Input sequences
• second_aln (Proteinalignment) – Second alignment for aligning multiple MSAs
• maintain_order (boolean) – Whether to maintain input order of sequences (default True)

Returns:

Aligned sequences

Return type:

ProteinAlignment

Dev note: - Unimplemented features: - - Speedup options