The software DeCo computes adjacencies (or any type of relation, like regulation, interaction, functional relationships) between ancestral genes from gene phylogenies reconciled with a species phylogeny according to duplications and losses. It takes as input (1) a species tree (2) a set of extant genes (3) a set of exant adjacencies (relations) between extant genes and (4) gene trees which leaves are the extant genes. It outputs ancestral species, genes, and adjacencies. It also highlights the duplications involving several genes.
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Bioinformatics. 2012 Sep 15;28(18):i382-i388. doi: 10.1093/bioinformatics/bts374.
Evolution of gene neighborhoods within reconciled phylogenies.
Bérard S, Gallien C, Boussau B, Sz?ll?si GJ, Daubin V, Tannier E.