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Read This First - VERSION 2.0

This manual describes an interim release of ALSCRIPT that includes many additional features over the previously distributed Version 1.4.5. I had hoped to make a lot more changes and improvements before distributing the new version, however I have not had the time to do this. I am distributing Version 2.0 since the new features have been used in a number of published alignment figures. Please see New Features in Version 2.0 for details of the new features.