Subgenomes

For polyploidy events with evidence for signficant biased fractionation (currently all events save that in yeast), POInT can assign orthologous single-copy genes to subgenomes, which are inferred to derive from one of the two allopolyploid parents. In the case of single-copy orthologys, the confidence in this assignment is the same as the overall "pillar" confidence. Hence, when single-copy orthologs are requested from the download engine, you have the option of requesting all such orthologs, or only those deriving from the subgenome that is least fractionated (has the most surviving genes) or the most fractionated subgenome (fewest surviving genes). For the hexaploids, there is also a subgenome of intermediate fractionation.