MUSCLE
MUSCLE was described in [Edgar, 2004b] and [Edgar, 2004a]. See http://www.drive5.com/muscle/muscle.html to find the various command line options.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).
Figure 2.5: Setting MUSCLE alignment parameters
When using the MUSCLE program, there is only one output, that is an alignment file.