Free Software

BioEdit - a very popular free sequence alignment editor for Windows.

Staden Package - a powerful open source sequence assembly and editing package for UNIX, Linux, Windows, and Mac OS X. Not the most user-friendly package, steep learning curve.

Se-Al - An older sequence alignment editor for Mac OS X. Not updated since 2002, but still popular.

4Peaks - A free trace viewer and editor for Mac OS X.













Commercial Software

CodonCode Aligner - A powerful sequence assembly program for Windows and Mac OS X. Free demo downloads (no forms), 30-day fully functional trial. Published prices, significantly less expensive than other popular packages.

Sequencher - Perhaps the most commonly used package in the USA. Prices for licenses are not listed at the web site, but typically start at several thousand dollars.

DNASTAR Lasergene - Another popular sequence assembly program. Similar in price to Sequencher. Trials and prices available only through web forms.












Sequence Assembly Software

This site is dedicated to software for DNA sequence assembly and alignment. Sequence assembly refers to the process of merging DNA fragments into larger "contigs" for subsequent analysis. An overview of different problems and approaches is available on Wikipedia.

Free and Open Source Sequence Assembly Programs

Gap4 / Gap5 Open source sequence assembler for Sanger sequencing. Part of the Staden package of DNA sequence analysis tools.

The sequence assembly program Phrap was developed to assemble shotgun cosmid and BAC sequencing projects in the Human Genome Project. Phrap pioneered a number of important idea, including the automatic use of entire sequences without trimming and accurate consensus sequences based on sequence qualities and confirmation by other reads.
Free for academic research use.

Celera Assembler The program that was used to assemble the first human genome, released as open source in 2004. Assembles Sanger sequencing data and Roche 454 data.
Arachne A whole genome assembler for Sanger sequencing reads developed at the Broad Institute. Free for research and educational use.
ALLPATH A sequence assembly program for whole genome assemblies from short ("next generation") sequencing reads from MIT's Broad Institute. Free for research and educational use.
MUMmer An open source software package for aligning whole genomes.
AMOS A Modular, Open Source whole genome assembler. A collaboration of four research institutes.

Genome Assembly Benchmark Data

The Center for Bioinformatics and Computational Biology at the University of Maryland has compiled a collection of sequence data from several bacterial genomes for benchmarking sequence assembly software.

Please note that this site is currently under construction - please check back in a few days for more information.