Vector NTI - Gained popularity when the program was made freely available to academic users, a policy that was ended in 2008.

Trials available through web forms, prices comparable to Sequencher (depending on the number of modules purchased). Has separate modules for sequence assembly and multiple sequence alignments, as well as other modules for primer design, gene finding, and sequence editing. A demo version is available after filling out a web form, but does not allow saving.ĭNASTAR Lasergene / MegAligner - Another popular program. Prices for licenses are not listed at the web site, but typically start at several thousand dollars. Sequencher - A widely used sequence alignment and assembly package that started out as a program for the 'classic' Macintosh. Commercial Software For Sequence Alignment 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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