Supplementary material for the work: Reconstructing Ancestral Genomic Sequences by Co-Evolution

The phylogenetic tree analyzed in this paper in Newick format.
A picture of the phylogenetic tree used in this work with branch lengths.
A table with COG groups, their phyletic pattern, their functional annotation.
The protein interaction network of E. coli.
The protein interaction network of S. cerevisiae.
The AND PPI graph for the two pp-networks.
Ancestral genomes inferred by ancestral co-evolver, by maximum parsimony, and by maximum likelihood.
The list of enzymes in each organisms.
The metabolic networks of all the organism .
The AND metabolic network for edges that appear in more than 10% of the organisms.
The AND metabolic network for edges that appear in more than 50% of the organisms.
Ancestral enzymes inferred by ancestral co-evolver, by maximum parsimony, and by maximum likelihood.
GO enrichment analysis for the proteins (COG dataset) found by ancestral co-evolver
GO enrichment analysis for the proteins (KEGG dataset) found by ancestral co-evolver and by maximum likelihood