Table 1.

Summary of published software for taxonomic classification and binning

Overall purpose	Software	Citation
Taxonomic classification and tree-building (using specific markers)	CheckM	[1]
	PhyloSift	[2]
	GToTree	[3]
	phyloSkeleton	[4]
Taxonomic classification at the contig level	Kaiju	[5]
	Kraken	[6]
	CLARK	[7]
	FOCUS	[8]
	MEGAN	[9]
	BlobTools	[10]
Taxonomic classification at the contig level (using all predicted genes)	CAT	[11]
	Mmseqs2	[12]
Binning with sequence compositional data	MetaBAT	[13]
	MaxBin	[14]
	Concoct	[15]
	BinSanity	[16]
	VizBin	[17]
Binning with sequence compositional data and taxonomic information	Anvi’o	[18]
	BlobTools	[10]