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Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.

Makes available various bioinformatics algorithms, which perform all essential tasks in sequence analysis and sequence-based predictions.

Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.

basecaller / assembler / sequencer finisher and related tools from the UW Genome Center.

Developers of software for real time PCR primer design, TaqMan, molecular beacons, DNA microarray analysis, drawing restriction plasmid maps, gateway cloning experiments, protein interaction network and functional genomics.

Software and an online service for periodically performing predefined searches at NCBI, reporting new results by email or on the web.

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.

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