For windows and OSX, current versions of DNADynamo instal a copy of Clustalw and Muscles for use by DNADynamo. On windows, the executables for these programs are
saved in the 'DNADynamo Installation Folder'. You can open this folder using the option under the 'Help' menu. For OSX, these programs are contained in the 'Resources'
folder within the DNADynamo application package.
For LINUX, you must place an executable for clustalw and muscle that are appropriate for your flavour of linux in the DNADynamo folder that also contains your
DNADynamo.jar executable file.
DNADynamo displays the raw output generated by clustalw or muscles during the alignment process in the 'Run Clustal' or 'Run Muscle' dialog
window that opens when you send sequences to be aligned. You can see the version of the software in this window.