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Bioinformatics. 2004 Jan 1;20(1):122-4.

GRIL: genome rearrangement and inversion locator.

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Department of Computer Science, University of Wisconsin-Madison, 1656 Linden Dr, Madison, WI 53706, USA.


GRIL is a tool to automatically identify collinear regions in a set of bacterial-size genome sequences. GRIL uses three basic steps. First, regions of high sequence identity are located. Second, some of these regions are filtered based on user-specified criteria. Finally, the remaining regions of sequence identity are used to define significant collinear regions among the sequences. By locating collinear regions of sequence, GRIL provides a basis for multiple genome alignment using current alignment systems. GRIL also provides a basis for using current inversion distance tools to infer phylogeny.


GRIL is implemented in C++ and runs on any x86-based Linux or Windows platform. It is available from

[Indexed for MEDLINE]

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