Table 1 Open in new tab Approaches for...

Approach

MGS Specific^a

Example Implementations

Identify outlier genomic regions based on DNA composition

GIST (Hasan et al. 2012); IslandViewer (Bertelli et al. 2017)

Identify outlier genes in contigs based on pairwise Pearson correlations of k-mer content

Yes

Described in Tamames and Moya (2008)

Identify genes in genomes displaying taxonomically discordant similarity to genes within a reference database

DarkHorse (Podell and Gaasterland 2007); HGTector (Zhu et al. 2014)

Identify genes in contigs displaying taxonomically discordant similarity to genes within a reference database

Yes

WAAFLE^b and a method described in Tamames and Moya (2008)

Reconcile phylogenetic incongruencies between gene and species trees

AnGST (David and Alm 2011); RANGER-DTL (Bansal et al. 2018)

Identify putative donor and recipient transfer events within a given community based on a combined similarity and phylogenetic incongruency approach

Yes

MetaCHIP (Song et al. 2019)

Identify genomic hotspots of recombination between strains of a species

Yes

Described in Tyson et al. (2004) and Probst and Banfield (2018)

Table 1

Approaches for Identifying Putative Cases of HGT in Metagenomes

Approach	MGS Specific^a	Example Implementations
Identify outlier genomic regions based on DNA composition	No	GIST (Hasan et al. 2012); IslandViewer (Bertelli et al. 2017)
Identify outlier genes in contigs based on pairwise Pearson correlations of k-mer content	Yes	Described in Tamames and Moya (2008)
Identify genes in genomes displaying taxonomically discordant similarity to genes within a reference database	No	DarkHorse (Podell and Gaasterland 2007); HGTector (Zhu et al. 2014)
Identify genes in contigs displaying taxonomically discordant similarity to genes within a reference database	Yes	WAAFLE^b and a method described in Tamames and Moya (2008)
Reconcile phylogenetic incongruencies between gene and species trees	No	AnGST (David and Alm 2011); RANGER-DTL (Bansal et al. 2018)
Identify putative donor and recipient transfer events within a given community based on a combined similarity and phylogenetic incongruency approach	Yes	MetaCHIP (Song et al. 2019)
Identify genomic hotspots of recombination between strains of a species	Yes	Described in Tyson et al. (2004) and Probst and Banfield (2018)

Approach	MGS Specific^a	Example Implementations
Identify outlier genomic regions based on DNA composition	No	GIST (Hasan et al. 2012); IslandViewer (Bertelli et al. 2017)
Identify outlier genes in contigs based on pairwise Pearson correlations of k-mer content	Yes	Described in Tamames and Moya (2008)
Identify genes in genomes displaying taxonomically discordant similarity to genes within a reference database	No	DarkHorse (Podell and Gaasterland 2007); HGTector (Zhu et al. 2014)
Identify genes in contigs displaying taxonomically discordant similarity to genes within a reference database	Yes	WAAFLE^b and a method described in Tamames and Moya (2008)
Reconcile phylogenetic incongruencies between gene and species trees	No	AnGST (David and Alm 2011); RANGER-DTL (Bansal et al. 2018)
Identify putative donor and recipient transfer events within a given community based on a combined similarity and phylogenetic incongruency approach	Yes	MetaCHIP (Song et al. 2019)
Identify genomic hotspots of recombination between strains of a species	Yes	Described in Tyson et al. (2004) and Probst and Banfield (2018)

Whether an approach is intended specifically for shotgun metagenomics (MGS) data instead of isolate genomes.