Table 1 Summary of published software for taxonomic classification and binning

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]