data/Francesca_Science06_133_genomes.path.txt
==========================
This file listed 133 ptt file paths for the genomes studied by Francesca et al.


data/Francesca_Science06_133_genomes
==========================
This folder contained 133 ptt files for the genomes listed in the file data/Francesca_Science06_133_genomes.path.txt


data/Francesca_Science06_133_genomes.info.txt
==========================
This file listed the information of the 133 analyzed genomes.
It was used to associate the taxonomy ID (column 1) of the above tree node, with NCBI's sequence accession ID (column 2)


data/tree_Feb15_midpoint_rooted.txt
==========================
This file contained the Newick formated phylogeny of the 191 genomes studied by Francesca et al.
It was originally downloaded from: http://www.bork.embl.de/tree_of_life/


data/RegulonDB_operon.cog
==========================
This file listed the 650 COG clusters of RegulonDB known operons in E. coli.
It was used to search the operon's occurrence in other genomes.

data/COG_functional_categories.xls
==========================
This file listed the information of the COG function category annotation codes.
It was originally downloaded from: http://www.ncbi.nlm.nih.gov/COG/grace/fiew.cgi