GeneDoc is described as 'A full featured multiple sequence alignment editor, analyser and shading utility for Windows'. There are five alternatives to GeneDoc for a variety of platforms, including Mac, Windows, Linux, Online / Web-based and Self-Hosted solutions. The best alternative is UGENE, which is both free and Open Source. Other great apps like GeneDoc are Geneious (Paid), Clustal X (Free), Genophore (Free Personal) and CLC Main Workbench (Paid).
QIAGEN CLC Main Workbench is ideal for DNA, RNA, & protein sequence data analysis with a wide variety of features, no advanced computer skills required! The workbench is available for Windows, Mac OS X, and Linux platforms.