Vhybridize software contains Virtual Hybridization command line tools. Virtual Hybridization uses sets of short probes to generate datasets for comparative genomics: given a DNA sequence and a set of probes, the typical output will give a sequence of oriented probe hits along the DNA sequence.
Other tools are supplied to allow simple manipulations such as format conversion and extraction of permutations.
Typically, you'll select a probe set with pipviewer and use it to produce gene order datasets on multiples genones with Vhybridize.
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