Table 2.
The softwares and databases used for comparative analysis
| Analysis | Software/database | References | Clinically pathogenic strains | Environmental strains | Human‐associated strains | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PR63039 | CCUG 10230 | CCUG 12901 | CIP 101113 | CCUG 12700 | L41 | H1bi | CCUG 3837 | CCUG 39352 | Myroides sp. A21 | |||
| Sequence level | Complete | Scaffold | Scaffold | Scaffold | Scaffold | Contig | Contig | Scaffold | Contig | Complete | ||
| Phylogenetic tree | REALPHY | Bertels, Silander, Pachkov, Rainey, & van Nimwegen, 2014; | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes | Yes |
| CG | CG viewer | Grant & Stothard, 2008; | Yes | Yes | Yes | Yes | ||||||
| ISs | IS Finder | Siguier, Perochon, Lestrade, Mahillon, & Chandler, 2006; | Yes (43) | Yes (169) | Yes (117) | Yes (104) | ||||||
| Synteny | Progressive mauve | Darling et al., 2010; | Yes | Yes | Yes | Yes | Yes | Yes | Yes | |||
| Prophage | PHAST | Zhou, Liang, Lynch, Dennis, & Wishart, 2011; | Yes (2 incomplete) | Yes (2) | Yes (5) | Yes (1) | ||||||
| CRISPR | CRISPR Finder | Bland et al., 2007; | Yes (3) | Yes (4) | Yes (ND) | Yes (ND) | Yes (1) | Yes (ND) | Yes (1) | |||
| Antibiotic resistance genes | CARD Resistance Gene identifier | Mcarthur et al., 2013; Jia et al., 2017; | Yes | Yes | Yes | Yes | ||||||
| Virulence factors | VFDB protein Set B database | Chen et al., 2012, 2016 | Yes | Yes | Yes | Yes | Yes | Yes | ||||
CG, Circular genome maps (Genomic variants); ISs, insertion sequence elements; Yes, analyzed; (): number of the predicted; ND, not detected.