No graphical user interface public domain, available as source code. MUSCLE - A newer multiple sequence alignment program that often gives better alignments that Clustal, and is substantially faster for large data sets. Available with a graphical user interface (ClustalX) or with a command line interface (ClustalW). Free Sequence Alignment SoftwareĬlustal - Perhaps the most commonly used tool for multiple sequence alignments. Integrated web interface for BLAST searches and GenBank browsing. MEGA - A free tool for sequence alignment and phylogenetic tree building and analysis. Free demo downloads (no forms), 30-day fully functional trial. Has not been actively developed for several years, but still gets excellent reviews.ĬodonCode Aligner - A powerful sequence alignment program for Windows and Mac OS X. Sequence Alignment Software Editor's PicksīioEdit - a free and very popular free sequence alignment editor for Windows.
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