A widely-used program for base calling DNA sequencing trace files. Source code available and free for non-commecial users.

An integrated linux environment for bioinformatics and evolutionary analysis based on the Genetic Data Environment (GDE). Contains binaries for Linux and Mac OS X, documentation, screenshots, references, and organism specific interfaces.

Freeware DNA cloning, analysis and visualization software.

A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.

A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.

Search for Tandem Repeats IN Genomes. Includes C source code and examples.

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.

Free software for working with and managing nucleotide sequences in multiple formats. Features include sequence annotation, restriction analysis, pattern searching, retrieval from servers. Released under GNU Public Licence.

NSF supported project to make old computers accessible to new software in bioinformatics. Provides transitional and supplemental support, especially in structual biology, for software packages on various platforms.

A graphical user interface for linear modelling of cDNA and oligonucleotide microarray data to identify differentially expressed genes.