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GeneMine

download alignment and structure visualization software.

GeneMine is now open source: GeneMine is now open source and no longer requires any license at all. Just compile the code and you'll be good to go. I don't have the docs on me right now but the process is very simple:
GeneMine source code: GeneMine source code. $ tar xvf gm352src.tar
GeneMine installer: GeneMine installer. $ tar xvf gm352_install.tar