Table 1. Web services and standalone software tools for taxonomic purposes.

Tool	Algorithm	Function	Type	URL	Reference
ANI calculator (Kostas lab)	ANIb	Calculation of ANI	Web service	http://enve-omics.ce.gatech.edu/ani/	[27]
ANI calculator (EzBioCloud) and OrthoANIu	Orthologous ANIu	Calculation of ANI	Web service and standalone	https://www.ezbiocloud.net/tools/ani https://www.ezbiocloud.net/tools/orthoaniu	[66]
JspeciesWS	ANIb, ANIu, Tetra correlation	Calculation of ANI and Tetra-Nucleotide Analysis	Web service	https://jspecies.ribohost.com/jspeciesws/	[67]
FastANI	Mashmap/MinHash	Calculation of ANI	Standalone	https://github.com/ParBLiSS/FastANI	[68]
Genome-to-Genome Distance Calculator	GBDP	Calculation of dDDH	Web service	https://ggdc.dsmz.de/ggdc.php#	[41]
Type (Strain) Genome Server	GBDP	Calculation of dDDH, 16S phylogenetic tree reconstruction, phylogenomic tree reconstruction, genome-based classification	Web service and API	https://tygs.dsmz.de/	[40,41]
AAI calculator (Kostas lab)	blastp	Calculation of AAI	Web service	http://enve-omics.ce.gatech.edu/aai/	[27]
EzAAI	MMSeqs2	Calculation of AAI	Standalone	http://leb.snu.ac.kr/ezaai	[28]
MIGA	Pipeline with several algorithms	Assembly, calculation of ANI, AAI, genome-based classification (based on AAI or ANI)	Web service	http://microbial-genomes.org/	[69]
Global Catalogue of Type Strain (gcType) Platform	Pipeline with several algorithms	Assembly, annotation, 16S phylogenetic tree reconstruction, phylogenomic tree reconstruction, genome-based classification	Web service	https://gctype.wdcm.org/	[70]
POCP (Hoelzer)	blastp	Calculation of POCP	Standalone	https://github.com/hoelzer/pocp	[17]
POCP-matrix (Bio-py)	blastp	Calculation of POCP	Standalone	https://github.com/SilentGene/Bio-py/tree/master/POCP-matrix	[17,71]
GTDBtk	Pipeline with several algorithms	phylogenomic tree reconstruction, genome-based classification	Standalone	https://github.com/Ecogenomics/GTDBTk	[48]
PhyloPhlAn	Configurable with multiple algorithms	Phylogenomic tree reconstruction	Standalone	https://segatalab.github.io/tools/phylophlan/	[72]
IQTree	Configurable with multiple models	Maximum likelihood phylogenomic tree reconstruction from alignment	Web service and standalone	http://www.iqtree.org/	[73]
UBCG	Pipeline with several algorithms	Phylogenomic tree reconstruction of Bacteria	Standalone	https://www.ezbiocloud.net/tools/ubcg	[35,38]
UACG	Pipeline with several algorithms	Phylogenomic tree reconstruction of Archaea	Standalone	https://www.ezbiocloud.net/tools/uacg	[36]
BBMap	Multi-kmer-seed-and-extend	Calculation of sequencing depth of coverage	Standalone	https://sourceforge.net/projects/bbmap/	[74]
ContEst16S	Pipeline with several algorithms	Contamination check (16S)	Web service	https://www.ezbiocloud.net/tools/contest16s	[58]
CheckM	Pipeline with several algorithms	Calculation of completeness and contamination	Standalone	https://github.com/Ecogenomics/CheckM	[60]
CheckM2	Pipeline with several algorithms, improved with machine learning	Calculation of completeness and contamination	Standalone	https://github.com/chklovski/CheckM2	[62]
busco	Pipeline with several algorithms	Calculation of completeness and contamination	Standalone	https://busco.ezlab.org/	[61]
Kbase	Web based server with multiple programs	Server hosting multiple programs with taxonomic utility	Web service	https://www.kbase.us/	[75]