Table 2.

Overview of the reference data sets

Category	Name	# Sequences	Average sequence length	# Files	# Sequence comparisons
Regulatory element detection	Cis-regulatory modules (CRMs) [6]	370	764 nt	370	68,256
Protein sequence classification	Low sequence identity (< 40%) [57]	1,066	180 aa	1,066	567,645
	High sequence identity (≥ 40%) [57]	2,128	184 aa	2,128	2,263,128
Gene tree inference	SwissTree [58]	651	398 aa	651	211,575
Genome-based phylogeny	Assembled genomes
	29 E. coli/Shigella strains	29	4,895,247 nt	29	406
	14 plant species	14	337,515,688 nt	14	91
	25 fish mitochondrial genomes [59]	25	16,623 nt	25	300
	Unassembled genomes
	29 E. coli/Shigella strains
	Coverage 0.03125	29,557	150 nt	29	406
	Coverage 0.0625	59,116	150 nt	29	406
	Coverage 0.125	118,266	150 nt	29	406
	Coverage 0.25	236,541	150 nt	29	406
	Coverage 0.5	473,081	150 nt	29	406
	Coverage 1	946,169	150 nt	29	406
	Coverage 5	4,730,778	150 nt	29	406
	14 plant species
	Coverage 0.015625	48,274	150 nt	14	91
	Coverage 0.03125	96,489	150 nt	14	91
	Coverage 0.0625	1,931,268	150 nt	14	91
	Coverage 0.125	3,862,905	150 nt	14	91
	Coverage 0.25	7,725,928	150 nt	14	91
	Coverage 0.5	15,461,718	150 nt	14	91
	Coverage 1	30,903,727	150 nt	14	91
Horizontal gene transfer	27 E. coli/Shigella genomes [60]	27	4,905,896 nt	27	351
	8 Yersinia species [61]	8	4,605,553 nt	8	28
	33 simulated genomes [62]
	HGT level 0	33	2,205,524 nt	33	528
	HGT level 250	33	2,149,620 nt	33	528
	HGT level 500	33	2,230,317 nt	33	528
	HGT level 750	33	2,263,926 nt	33	528
	HGT level 1,000	33	2,238,661 nt	33	528

An interactive visualization of all results for all data sets can be found online (http://afproject.org)