Table 2.

Description of the Score between Leaves

note.—The two parameters F_adj and SPI used in the scaffolding modes, respectively, account for the position of the genes in their contig and the repartition of poorly assembled genomes in the species tree; both parameters are described with more details in the supplementary material, Supplementary Material online. The scaffolding mode and score given option can be used simultaneously as they affect a different set of adjacencies: respectively, the adjacencies absent from the input and the adjacencies given in the input.