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gview 5.0 Free

GView is a Java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file.

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TopHat Free

TopHat is a fast splice junction mapper for RNA-Seq reads.

mammalian-sized genomes using...analyzes the mapping 

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KegArray Free

KegArray - Java application for microarray data analysis.

to easily map...BRITE and genome maps 

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