MUSCLE
MUSCLE is described in [Edgar, 2004b] and [Edgar, 2004a]. See http://www.drive5.com/muscle/muscle.html to find the detailed user guide.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 Specify the maximum memory to be allocated. Exceeding the default value (1000 Mb) is not recommended.
Figure 2.5: MUSCLE alignment options
MUSCLE produces a single alignment as an output.