schrodinger.protein.tasks.muscle module¶

schrodinger.protein.tasks.muscle.get_muscle_path()¶

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.

class schrodinger.protein.tasks.muscle.MuscleJob(aln, second_aln=None, quiet=True, maintain_order=True, seqtype='auto')¶

Runs alignment via MUSCLE program

Note: Muscle by default rearranges the order to put similar sequences together

__init__(aln, second_aln=None, quiet=True, maintain_order=True, seqtype='auto')¶

Parameters

aln (ProteinAlignment) – Input sequences
second_aln (ProteinAlignment) – Second alignment for aligning multiple MSAs
maintain_order (bool) – Whether to maintain input order of sequences
seqtype – Sequence type. One of ‘auto’, ‘protein’, ‘rna’ or ‘dna’. In ‘auto’ mode, if >95 of the first 100 letters correspond to nucleotides, the file is treated as the relevant nucleotide type. Otherwise, it is treated as protein.

Dev note: - Unimplemented features: – Speedup options

run()¶

Run the MUSCLE alignment.