Mauve

Mauve aligns multiple draft or finished genome sequences, identifying conserved, lineage-specific, and rearranged genomic regions to support comparative genomics analyses of recombination, horizontal gene transfer, deletions, and large-scale rearrangements.

Key Features:

• Multiple genome alignment: Performs alignments across multiple genomes to detect conserved and variable regions.
• Support for draft and finished sequences: Accepts both draft and finished genome assemblies as input.
• Detection of segment types: Identifies conserved segments shared across all genomes, regions shared with subsets of genomes, and unique lineage-specific segments.
• Handling of rearrangements: Aligns genomic DNA despite rearrangements and the shuffling of linear segment order among genomes.
• Robustness to evolutionary processes: Accounts for recombination, horizontal gene transfer, and deletions that affect genome structure.
• Advanced algorithms for conserved-region alignment: Employs algorithms that identify and align conserved genomic DNA in the presence of rearrangements and horizontal transfers.
• Evaluation by simulation: Alignment quality and accuracy have been assessed using extensive simulations of genome evolution.

Scientific Applications:

• Comparative genomics: Enables comparative analyses of genome structure and content across multiple species or strains.
• Genome evolution studies: Facilitates investigation of the roles of recombination, horizontal gene transfer, deletions, and rearrangements in genome evolution.
• Enterobacterial genome comparison: Has been applied to align nine enterobacterial genomes to study evolutionary relationships and structural variation.
• Mammalian genome rearrangement analysis: Has been used to determine global rearrangement structure within three mammalian genomes.

Methodology:

Uses algorithms that identify and align conserved genomic DNA across genomes despite rearrangements and horizontal transfers, with alignment performance assessed by extensive simulations of genome evolution.