This dialog box contains a set of parameters for running MUSCLE to align PROTEIN sequences. If you wish to align DNA sequences then you must un-translate to DNA (assuming you started with DNA) then align.
Below are descriptions of some of the parameters you may change, if you do not change them they will stay as whatever you see them at last.
Presets:
None: Not selecting any presets
Large Alignment: If you have a large number of sequences (a few thousand) or they are very long the default settings may be too slow for practical use. This sets the max number of iterations to 2. (command parameter: -maxiters 2)
Fast Speed: Gives the fastest possible speeds for a result. This will compromise on accuracy. (command parameters: -maxiters 1 -diags -sv -distance1 kbit20_3)
Refining Alignment: Use this when you are refining an existing alignment to make it better. (command parameters: -refine)
Gap Opening Penalty: The penalty for opening a gap in the alignment. Increasing this value makes the gaps less frequent.
Gap Extension Penalty: The penalty for extending a gap by one residue. Increasing this value will make the gaps shorter. Terminal gaps are not penalized.
Hydrophobicity Multiplier: Multiplier for gap open/close penalties in hydrophobic regions.
Max Memory in MB: MUSCLE by default specifies an upper limit on how much of your computer's memory it may use (in Megabytes) so that it does not use all your computers resources and cause it to run slow or be unable to operate. By default this number is how much physical memory your computer has available. You may be able to increase this number depending on how much virtual memory you have available.
Max Iterations: The maximum number of iterations allowed
Clustering Method (Iteration 1,2): The clustering method used in the first two iterations.
Cluster Method (Other Iterations): The clustering method used in iterations after the first two.
Max Diagonal Length: Maximum length of the diagonal
Other Commands: You may enter parameters for MUSCLE which will be appended to the previously selected parameters.