Fig. 1

Input and output of ADSEQ. (Left) Input data: (1) a species tree with extant genomes (A, B and C) containing observed adjacencies (black link) and scaffolding gene adjacencies with a prior score (blue link); each grey box represents a gene. (2) reconciled gene trees representing evolutionary histories of gene families annotated by evolutionary events. (Right) Typical output: gene order across ancestral and extant genomes including new extant gene adjacencies with a posterior score (green link) between genes located at fragments extremities in the initial genome assemblies