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The Washington University improved version of BLAST. Free for academic users.
http://blast.wustl.edu/
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Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
http://www.seqtools.dk
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Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 & XP.
http://www.immunokin.com
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Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics.
http://www.premierbiosoft.com/
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DNA sequence assembler and finishing tools from the UW Genome Center.
http://www.phrap.org/
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Freeware DNA cloning, analysis and visualization software.
http://www.acaclone.com
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Offers a range of free software tools for annotating an entire genome, assembling sequences, gap closing and analysis of microarrays.
http://nbc3.biologie.uni-kl.de
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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.
http://metameme.sdsc.edu/
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Software for simulating metabolic, signal and genetic networks. Home of Jarnac, JDesigner and SCAMP.
http://sbw.kgi.edu/
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Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
http://jaligner.sourceforge.net/
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Profiles protein sequence data using hidden Markov models of a statistical descriptions of a sequence family's consensus. HMMER is a freely distributable implementation of profile HMM software for protein sequence analysis.
http://hmmer.wustl.edu/
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Commercial Windows software for analyzing biochip image data.
http://www.genespotter.de
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William Pearson's package for fast sequence comparison tools.
ftp://ftp.virginia.edu/pub/fasta
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A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product - now "abandonware."
http://www.generunner.com
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An Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
http://dnptrapper.sourceforge.net/
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