Readme for the Brassica WGT ancestral genome reconstruction.
As described in the corresponding manuscript, the order of the genes just prior to the Brassica WGT was inferred (BrassicaWGT_inferred_anclocorder.txt). These genes were identified with their Arabidopsis thaliana orthologs (BrassicaWGT_inferred_anc_locIDs.txt). We then used both this order (BrassicaWGT_AncOrder_POInT_Pillars.txt) and an optimized one (BrassicaWGT_AncOrder_POInT_OptPillars.txt) to fit models of post-hexaploidy gene loss using POInT. The corresponding gene order files are also provided here: the model files and phylogenetic topologies in the parent directory can be used for all POInT analyses.