muscle

Muscle is a multiple sequence alignment tool capable of assembling high accuracy alternative alignments. It accepts FASTA as input and outputs an aligned FASTA. It detects the number of CPUs available for processing and will use up to 20 by default.

For more information see the documentation

ml biocontainers muscle
muscle --align input.fasta --output output.fasta

Parallel Capabilities: Multithreading options supported.