Sequence Alignment Software
Editor's Picks
BioEdit - a free and very popular free sequence alignment editor for Windows. Has not been actively developed for several years, but still gets excellent reviews.
CodonCode Aligner - A powerful sequence alignment program for Windows and Mac OS X. Free demo downloads (no forms), 30-day fully functional trial.
MEGA - A free tool for sequence alignment and phylogenetic tree building and analysis. Integrated web interface for BLAST searches and GenBank browsing.
Free Sequence Alignment Software
Clustal - Perhaps the most commonly used tool for multiple sequence alignments. Available with a graphical user interface (ClustalX) or with a command line interface (ClustalW).
MUSCLE - A newer multiple sequence alignment program that often gives better alignments that Clustal, and is substantially faster for large data sets. No graphical user interface; public domain, available as source code.
Se-Al - An older sequence alignment editor for Mac OS X. Not updated since 2002, but still popular.
JAligner - Java implementation of the Smith-Waterman algorithm for pairwise alignments.
Mesquite - Software for evolutionary biology. Most functions are for post-alignment analysis like phylogenetic tree analysis, but also useful to view and manipulate sequence alignments.
Commercial Software For Sequence Alignment
Sequencher - A widely used sequence alignment and assembly package that started out as a program for the "classic" Macintosh. Prices for licenses are not listed at the web site, but typically start at several thousand dollars. A demo version is available after filling out a web form, but does not allow saving.
DNASTAR Lasergene / MegAligner - Another popular program. Has separate modules for sequence assembly and multiple sequence alignments, as well as other modules for primer design, gene finding, and sequence editing. Trials available through web forms, prices comparable to Sequencher (depending on the number of modules purchased).
Vector NTI - Gained popularity when the program was made freely available to academic users, a policy that was ended in 2008. The current (4/18/09) list price for a 3-year academic license for Vector NTI is $1975.00 (with discounts of about 30% being offered).
MacVector - Another program package with many functions that has been around for a long time. Academic licenses cost $2,000, with discounts for additional licenses. However, advanced assembly based on PHRAP requires additional license fees.
CodonCode Aligner - Newer software for sequence alignment and sequence assembly on Windows and Mac OS X. Free trial downloads. Published prices, significantly less expensive than other popular packages. One useful and unique feature is the ability to align assembled contigs with Clustal or MUSCLE to create "contigs of contigs".