Muscle

Overview

• Muscle: Muscle v5 is a major re-write of MUSCLE based on new algorithms. Alignment ensembles : Muscle v5 can generate ensembles of high-accuracy alternative alignments. All replicates have equal average accuracy on benchmark test, including the MSA made with default parameters. By comparing results of downstream analysis (trees, structure prediction...) on different replicates, you can assess the effects of alignment errors on your study.

Using

Use the module name muscle to discover versions available and to load the application.

Multicore

A number of the muscle commands allow you to use multiple cores. Please check the align and super5 documentation to read about the -threads options.