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There are various powerful (non-interactive) programs for drawing the awesome pictures that you see in . These tools are easiest to install on a computer where you have administrator privileges. publications. They are not CPU intensive and you have to fiddle with the configuration files, so it's best to use them on your own computer where you can easily view the images that they create. These tools are also easiest to install on a computer where you have administrator privileges.
- Circos - fully featured. Very cool functions for drawing connections between different chromosome locations.
- CGView Simpler to use. Better functionality for showing genes up close as arrows. Does not draw links.
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If you are going to seriously annotate a eukaryotic genome, then you are going to need a machine with database infrastructure and other tools installed. Here are two systems for annotating gene structure in eukaryotic genomes as examples:
PASA - Program to Assemble Spliced Alignments
CEGMA - Core Eukaryotic Genes Mapping Approach