![]() ![]() Most functions are for post-alignment analysis like phylogenetic tree analysis, but also useful to view and manipulate sequence alignments. Mesquite - Software for evolutionary biology. JAligner - Java implementation of the Smith-Waterman algorithm for pairwise alignments. Not updated since 2002, but still popular. Se-Al - An older sequence alignment editor for Mac OS X. 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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