I think you'll struggle to find free or open source GUI based aligners for 454 data.
Perhaps you can get a copy of Newbler from Roche, else work with a trial version of CLC genomics etc.
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Aligning 454 data to a reference sequence
I am trying to align my 454 data that I received to my sanger sequences that I did previously. I am trying to just look at intra-individual virion diversity. All I need to do is see how many different sequences are present in each individual and how often they occur. I have tried several programs, but they all want to do more complicated things. I am currently trying to run this in the program UGENE because it is free, I have it on my computer, and it is not command line run. Does anyone know how to do this simple task in this program?!
Thanks!
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