• Chemical Simulations Group
Software and consulting services to the pharmaceutical, biotechnology, and chemical industries.
• Linux for Biotechnology
LfB - V1 includes over 1Gb of Biotechnology related software, all precompiled for Linux (x86), in easy to install RPM format. A range of state-of-the-art tools for sequence analysis, and molecular visualization and modelling.
• Tripos, Inc.
Provider of discovery research software & services to pharmaceutical, biotechnology, & other life sciences companies worldwide.
• GeneRunner for Windows
A fairly old sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
• HMMER Profile Hidden Markov Models for Sequence Analysis
Sean Eddy's tools to build HMMs from multiple alignments, align sequences to HMMs, calculate e-scores, and other tools
• Logical Depth
Accelerated sequence analysis tools for HMMsearch and Smith-Waterman.
• Molecular Evolutionary Genetics Analysis (MEGA2) software
Provides free downloadable MEGA2 software for use in comparative sequence analysis of genetic data. Program for Win32 platforms.
• PHRED: Base-Calling Software with Quality Information
A widely-used program for calling DNA sequence bases from sequencer trace files.
• Sequence Analysis for Mac OS X
A freeware Mac OS X application written in Java that does many standard types of DNA and protein sequence analysis tasks.
• Verbumculus Genetic Sequence Analyzer
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.
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