Data and code of "Deciphering the Ancestral Evolution of the Paleo-hexaploidized Solanaceae Genome".

code: Contains code for construction of virtual genome, identification of syntenic fragment, and identification of intra-genome synteic gene pairs.

representative_subgenome: Three sets of tomato sub-genomes are compressed into a set of representative sub-genome. The folder contains the protein sequence file and gene location file of this genome.

virtual_genome: A virtual genome constructed using five non-solanaceous species genes. The folder contains the protein sequence file and gene location file of this genome.

SynOrths_V1.5: Syntenic analysis tool. (If used, please cite "Cheng F, Wu J, Fang L, Wang X. 2012. Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front Plant Sci. 3:198. doi: 10.3389/fpls.2012.00198".)

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