Fig. 4

The pipeline of MGA. a An example of large-scale genomic rearrangement, insertion, and deletion occurring across a set genomes. The lines denote bounds of homologous segments, and inversions are denoted by crossing lines. b Anchors from the section of 3 genomes surrounded by the dotted box in a. Once again, the lines between genomes represent homology. The labeled blocks on each genome correspond to anchors, where two blocks with the same label are inferred to be potentially homologous sites. c The alignment graph obtained by merging the 3 linear genome graphs in b. At this step, the aim of MGA is to find colinear paths in the graph i.e. sequences of anchors which are traversed by a group of genomes in the same order. d Often times, the initial set of anchors will be too noisy, containing spurious alignments which prevent the formation of longer, more reliable colinear paths. By removing anchor F, the alignment graph becomes much simpler and yields longer colinear paths, where each set of colinear paths is denoted by the color. e For each colinear path, MGA tools perform an MSA, yielding a set of sequence alignments which together make up the genome alignment