Fig. 4

Left: Number of segments in extant and ancestral genomes, according to three runs of ADSEQ in three different conditions. In the first run, we turn off the scaffolding mode on the X phylogeny, that is, it only constructs ancestral segments. The first column “XNS ext” thus describes the initial assembly, and “XNS anc” the assembly of ancestral genomes when reconstructed without extant scaffolding. In the second and third runs, the scaffolding mode was turned on, and run with the X phylogeny (“X ext” and “X anc”) and the WG phylogeny (“WG ext” and “WG anc”). Right: Number of rearrangements over all branches of the X phylogeny, with and without the scaffolding mode