Table 4.

Description of the Empirical Data Sets Used in Our Benchmark.

Data Set	Families	Genes	GFTs	Gene Data Source
Primates13	16,670	268,338	Inferred	Ensembl Compara
Cyanobacteria36	1,099	41,035	Inferred	Hogenom
Vertebrates22	18,829	1,521,587	Extracted	PhylomeDB
Fungi16	7,180	85,866	Extracted	Butler et al. (2009)
Fungi60	5,665	391,471	Inferred	PhylomeDB
Plants23	21,469	1,652,464	Inferred	PhylomeDB
Life92	41,222	628,747	Inferred	Williams et al. (2020)
Archaea364	150	46,801	Inferred	Dombrowski et al. (2020)
Plants83	9,237	1,294,695	Extracted	1000k plants
Vertebrates188	31,612	3,725,332	Inferred	Ensembl Compara

Note.—Data set names are suffixed by the number of species in the respective data set. Families are the number of input gene families. Genes are the total number of gene copies in the data set. GFTs indicate if we inferred the GFTs (“inferred”) or if we extracted them from the data source (“extracted”). Gene data source is the database or the project/publication from which the GFTs and/or gene family alignments were obtained.