Alternative to Muscle

[Dave Yarmosh]

Hi everyone,

ShortBRED is great and I'm including it in a common workflow of mine. I'm deviating from its initial purpose and using much larger datasets than just AMR genes. As such, the MSA step takes a very long time and is the bottleneck of my process. Muscle is not parallelizable -- does anyone know of an alternative that I could substitute in its place?

Thanks,
Dave