Abstract Summary: Mauve Contig Mover provides a new method for proposing the relative order of contigs that make up a draft genome based on comparison to a complete or draft reference genome. A novel application of the Mauve aligner and viewer provides an automated reordering algorithm coupled with a powerful drill-down display allowing detailed exploration of results. Availability: The software is available for download at http://gel.ahabs.wisc.edu/mauve. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online and http://gel.ahabs.wisc.edu

Abstract Summary: 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. Availability: GRIL is implemented in C++ and runs on any x86-based Linux or Windows platform. It is available from http://asap.ahabs.wisc.edu/gril Supplementary information: The GRIL web site contains a detailed description of the GRIL's algorithms, an example of applying GRIL to five genomes, and verification of the correctness of the results.