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- Jacques van Helden (ORCID 0000-0002-8799-8584)
- Etienne Decroly (ORCID 0000-0002-6046-024X)
- Erwan Sallard (erwan.sallard@ens.psl.eu)
- Didier Casane (http://www.egce.cnrs-gif.fr/?p=1289)
- José Halloy (ORCID 0000-0003-1555-2484)
- Web pages: https://jvanheld.github.io/SARS-CoV-2_origins/
- Git repository: https://github.com/jvanheld/SARS-CoV-2_origins
This repostiroy contains the code and data enabling to reproduce the results of our genoic and phylogentic analysis of SARS-CoV-2 origins, published in a French journal in August 2020, and whose English translation was published in Environmental Chemistry Letters in February 2021.
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E. Sallard, J. Halloy, D. Casane, J. van Helden, É. Decroly, Retrouver les origines du SARS-CoV-2 dans les phylogénies de coronavirus, Med Sci (Paris). 36 (2020) 783–796. https://doi.org/10.1051/medsci/2020123.
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E. Sallard, J. Halloy, D. Casane, E. Decroly, J. van Helden, Tracing the origins of SARS-COV-2 in coronavirus phylogenies: a review, Environ Chem Lett. (2021). https://doi.org/10.1007/s10311-020-01151-1.
| Contents | Type | doc |
|---|---|---|
| Installation and usage | manual | INSTALL-and-USE.md |
| Full-genome PIP profiles | report | [html] [Rmd source] |
| PIP profiles of genomic features (1-to-n matches) | report | [~20 strains] [~40 strains] [~60 strains] [Rmd source] |
| PIP profiles of spike protein sequences | report | [~20 strains] [~40 strains] [~60 strains] [Rmd source] |
| Phylogeny inference | report | [html] [Rmd source] |