GenomeTools is a collection of algorithms to manipulate genomics related file format. The primary purpose is to convert file formats from one to another.
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README.md

genometools

GenomeTools is a suite of tools to work with genomics data files.

More detailed information for each of these tools can be found in the tool descriptions.

Latest build is always available: http://genomeview.org/jenkins/genometools/

Start by using: java -jar genometools-.jar