# Whole-Genome Alignment: Methods, Challenges, and Future Directions
## 2 Classification of Whole-Genome Alignment Algorithms
### Anchor-Based Methods
#### 2.2.2. Mauve  
Mauve is a genome alignment method which is able to identify entire similar regions between a set of genomes, such as rearrangements, translocation, and inversions, and the exact breakpoints of each rearrangement across multiple genomes [27]. Therefore, Mauve is primarily used for aligning and comparing multiple genomes from different species. It helps researchers identify conserved regions, rearrangements, and evolutionary events across genomes. Mauve uses a progressive alignment algorithm, and the main originality of this algorithm is that unlike the other multiple genomes' alignment methods, it uses a heuristic approach to predict whether the anchors represent a similar region between the genomes or only a similar region caused by random mutations. The experimental results made using the Progressive Mauve method shows that the algorithm was able to detect the genome and the core genome of species from Enterobacteriaceae family. In addition to the Mauve alignment algorithm, a visualization tool has been developed to display the whole-genome alignment that shows the rearrangement between the genomes. Mauve offers several features to analyze and visualize the alignment, including the ability to zoom in and out of the alignment, rearrange genomes for better visualization, and export alignment data in various formats. Mauve is a valuable tool for comparative genomics research, providing insights into genome evolution and conservation across multiple organisms or strains. However, it may have limitations in handling extremely large genomes or genomes with high levels of divergence. Users should be aware of these limitations and consider alternative approaches for analyzing such datasets [31]. The algorithm constructs a similarity graph based on shared regions among genomes and then uses heuristics to identify and extend locally collinear blocks (LCBs) that represent conserved segments across genomes. Content and rearrangement are the two main techniques that are used in this method to better detect variable genes; the first scores all possible configurations of alignment anchors across the set of genomes [32], and the second applies the hidden Markov model (HMM) for homology to predict similar subsequences caused by random mutations and reject them, as in the following steps:  
1. Finding multi-MUMs: While the algorithm detects anchors across multiple genomes comparison, some repetitive regions can occur several times in each genome as a duplication of those regions. The more aligned genomes there are, the more difficult it becomes to place each anchor in the correct place within the global alignment. To resolve this problem, Mauve uses multiple maximal unique matches (multi-MUMs) with a minimal length k as anchors. Those multi-MUMs are the exact matching subchains shared by two or more genomes that occur only once in each genome and that are bounded on either side by mismatched nucleotides. In addition, to detect other anchors of a length less than k, Mauve uses an anchoring technique that reduces k while looking for smaller anchors in the remaining unmatched regions. Figure 4: MUMmer and MUMmer 4 Pseudo-code. * Calculating a phylogenic guide tree: Mauve uses the genomes' similar regions indicated by the subset of multi-MUMs as a binary distance metric to build a phylogenetic guide tree using neighbor joining [25]. * Selecting a set of anchors: This step consists in the detection of homologous subsequences. These regions are called locally collinear blocks (LCBs). Each locally collinear block is a homologous region shared by two or more genomes and does not contain any rearrangement of similar blocks. * Recursive anchoring and gapped alignment: The previous step may not detect all the regions of homology between the genomes, as a minimum length \(k\) is required for a region to be considered as an LCB. To resolve this problem, two recursive anchoring techniques are performed.