Table 1.

Summary statistics of OrthoFinder vs pSONIC

	Split tetraploid into subgenomes		Unsplit tetraploid
	OrthoFinder	pSONIC	OrthoFinder	pSONIC
Total groups of orthologs	28,036	31,963	28,268	31,967
Total singleton groups	12,294	17,197	11,155a	17,258a
Tether groupsb	21,624	31,016	19,558	31,051
Species-specific groups	53	1,517	50	1,654

^aThe number of groups in which all diploid species contributed one gene and the tetraploid species contributed two genes are shown. There were an additional 2,624 gene groups produced by Orthofinder and 1,718 gene groups produced by pSONIC that were composed of a single sequence from all four species, including G. hirsutum.

^bTether Groups refer to those groups in which all diploid species have one or zero genes (or tandemly duplicated sets of genes) and the tetraploid species has two or fewer genes (or tandemly duplicated sets of genes).