Supplementary Data for "Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants"

Data for: Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants<br> This dataset contains the main computed data used in that work. Find below a list of packages and a summary of their content. Next, each package is described in detail. extant_eudicot_genomes.tar.bz2 : Genome sequence files. atoms.tar.bz2 : Computed atoms. syntenic_blocks.tar.bz2 : Files related to syntenic blocks found. syntenic_blocks_refined.tar.bz2 : Files related to syntenic blocks found after the family refinement process. ancestor.tar.bz2 : Files related to the reconstructed ancestor. #### extant_eudicot_genomes.tar.bz2 artichoke.gbk<br> coffee.gbk<br> grape.gbk <br> lettuce.gbk<br> sunflower.gbk<br> Customized/filtered genbank files of species. #### atoms.tar.bz2 ag100_ai30_al13_m100.atoms : Computed atoms, that is, a list of genes and their families. #### syntenic_blocks.tar.bz2 ag100_ai30_al13_m100.cog : Sequence of genes in each chromosome (Gecko3-DCJ input genomes format).<br> rgrape_q3_dcj_dcjBorderline8_dcjPenality0.25_dcjUseHeuristics_dT0_0_0_2__1_0_1_3 ... .gckz : Sequence of genes in each chromosome with computed syntenic blocks and local DCJ similarity (Gecko3-DCJ session format).<br> rgrape_q3_dcj_dcjBorderline8_dcjPenality0.25_dcjUseHeuristics_dT0_0_0_2__1_0_1_3 ... .clusters : Syntenic blocks found by Gecko3-DCJ (Gecko3-DCJ clusters export format). <br> #### syntenic_blocks_refined.tar.bz2 refoverlap_refsim.genesmap : Map of new refined gene families. Each line contains two values, the first one is the new (refined) family number and the second one is the old family number. refoverlap_refsim_refined.cog : Sequence of genes in each chromosome (Gecko3-DCJ input genomes format). refoverlap_refsim_refined.gckz : Sequence of genes in each chromosome with computed syntenic blocks and local DCJ similarity (Gecko3-DCJ session format). refoverlap_refsim_refined.clusters : Syntenic blocks found by Gecko3-DCJ (Gecko3-DCJ clusters export format). refoverlap_refsim_refined.acs : Syntenic blocks as ACSs (ANGES format). refoverlap_refsim_refined.clustersmap : Map of syntenic blocks IDs. Each line maps an ID in the refoverlap_refsim_refined.acs file to an ID in the refoverlap_refsim_refined.clusters file. #### ancestor.tar.bz2 eudicots_ACS_C1P_HEUR : ACSs selected to compose the reconstructed ancestor. eudicots_PQTREE_HEUR : PQ-tree representing the reconstructed ancestor.