| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited data | ||
| Genome sequences of H. pylori (Genbank accession number) | This paper | CP006820 - CP006827, CP058279 - CP058288, and CP058250 - CP058252. See Table S3 for details. |
| Software and algorithms | ||
| MEGA (v.10.1.8) | Tamura et al. (2013) | https://www.megasoftware.net/ |
| ClonalFrameML (v.1.12) | Didelot and Wilson (2015) | https://github.com/xavierdidelot/ClonalFrameML |
| jModeltest (v.2.1.10) | Posada (2008) | http://evomics.org/learning/phylogenetics/jmodeltest/ |
| BEAST2 (v2.5.0) | Bouckaert et al. (2014) | https://www.beast2.org/ |
| Chromopainter (v.2) | Lawson et al. (2012) | https://people.maths.bris.ac.uk/%7Emadjl/finestructure-old/chromopainter_info.html |
| fineSTRUCTURE (v0.1.0) | Lawson et al. (2012) | http://www.paintmychromosomes.com/ |
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