MUSCLE parameter settings
- Find Diagonals (faster for similar diagonals)
- Maximum iterations If you are aligning a large number of sequences or if the sequences are very long, it is advisable to limit the number of iterations. A good number in such cases is 2.
- Maximum hours Maximum time to run in hours. The actual time may exceed the requested limit by a few minutes. Decimals are allowed, so 1.5 means one hour and 30 minutes. When the maximum hours limit is met, MUSCLE will be terminated without producing any alignment.
- Maximum Memory in mb Set maximum memory to be allocated to run. It is not recommended to exceed the default value (1000 mb).
When using the MUSCLE program, there is only one output, that is an alignment file.