Mauve is a software package for aligning conserved genomic sequences across multiple genomes, even when they have undergone rearrangements and horizontal transfer. The method identifies and aligns conserved regions, rearrangements, and inversions in these regions across multiple genomes. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. The software uses a combination of anchoring and progressive alignment to align sequences, with the anchoring step identifying regions of local collinearity called locally collinear blocks (LCBs). These LCBs are then used to guide the alignment of the entire genome. Mauve's alignment algorithm is based on the progressive dynamic programming approach of CLUSTAL W and uses a phylogenetic guide tree to determine the optimal progression of sequences for alignment. The software has been evaluated through extensive simulations of genome evolution and has been shown to perform well compared to other alignment methods. Mauve is available for download and is designed to be user-friendly and sensitive when comparing genomes with significant rearrangements. The software has been used to align nine enterobacterial genomes and to determine the rearrangement structure of three mammalian genomes. The results show that Mauve can accurately align conserved regions and identify rearrangements, even in the presence of horizontal transfer and other evolutionary events. The software is also capable of visualizing the rearrangement structure of genomes and has been used to analyze the genomes of three mammals. Overall, Mauve is a powerful tool for aligning genomic sequences and identifying evolutionary events such as rearrangements and horizontal transfer.Mauve is a software package for aligning conserved genomic sequences across multiple genomes, even when they have undergone rearrangements and horizontal transfer. The method identifies and aligns conserved regions, rearrangements, and inversions in these regions across multiple genomes. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. The software uses a combination of anchoring and progressive alignment to align sequences, with the anchoring step identifying regions of local collinearity called locally collinear blocks (LCBs). These LCBs are then used to guide the alignment of the entire genome. Mauve's alignment algorithm is based on the progressive dynamic programming approach of CLUSTAL W and uses a phylogenetic guide tree to determine the optimal progression of sequences for alignment. The software has been evaluated through extensive simulations of genome evolution and has been shown to perform well compared to other alignment methods. Mauve is available for download and is designed to be user-friendly and sensitive when comparing genomes with significant rearrangements. The software has been used to align nine enterobacterial genomes and to determine the rearrangement structure of three mammalian genomes. The results show that Mauve can accurately align conserved regions and identify rearrangements, even in the presence of horizontal transfer and other evolutionary events. The software is also capable of visualizing the rearrangement structure of genomes and has been used to analyze the genomes of three mammals. Overall, Mauve is a powerful tool for aligning genomic sequences and identifying evolutionary events such as rearrangements and horizontal transfer.