Table 1.

Total orthologs found in each method separated by matrix occupancy.

Method			8 spp	90%	Full
Genome-guided	Genes	Total	9,757	2,211	434
		Min	5,389	1,963	434
	Amino Acids	Total	4,182,364	835,229	144,503
		Min	1,775,925	669,215	128,896
Agalma	Genes	Total	11,563	2,308	555
		Min	5,453	2,054	555
	Amino Acids	Total	4,420,707	797,333	182,368
		Min	1,568,329	613,538	168,157
Yang & Smith 1 to 1	Genes	Total	7,323	1,925	898
		Min	3,685	1,781	898
	Amino Acids	Total	2,408,802	789,203	361,901
		Min	1,129,993	628,190	310,283
Yang & Smith MO	Genes	Total	11,568	1,966	1,076
		Min	6,417	1,879	1,076
	Amino Acids	Total	4,362,686	857,857	456,597
		Min	2,009,430	687,942	380,988