A widely-used program for calling DNA sequence bases from sequencer trace files.

A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks.

An interesting tool to discover and visualize over- or under-represented words in genetic sequences. Executable for Sparc-Solaris, Sparc-Intel or Linux-Intel. Also available as a Java applet.

Software for life science discovery; enterprise-level data integration and desktop biologists.

Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.

Software for creating interactive keys for biology, taxonomy, medicine, and agriculture.

Software development for structural bioinformatics. Runs on Unix, Windows and MacOSX.

PAL library is a Java toolkit for determining evolutionary trends.

Sfold predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids. The web server version is free for academic use.

WU-BLAST: The Washington University BLAST. "...faster at any sensitivity, more sensitive at any speed, the first BLAST with gapped alignments and statistics."