https://github.com/andersen-lab/sars-cov-1_evolution

https://github.com/andersen-lab/sars-cov-1_evolution

Last synced: about 1 year ago
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• Host: GitHub
• URL: https://github.com/andersen-lab/sars-cov-1_evolution
• Owner: andersen-lab
• Created: 2021-09-16T20:32:16.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2022-10-26T23:19:33.000Z (over 3 years ago)
• Last Synced: 2025-02-01T06:25:05.056Z (over 1 year ago)
• Language: R
• Size: 1.09 MB
• Stars: 1
• Watchers: 5
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
#### Summary

In this repo we are linking to various material that have to do with our investigations of the origin and evolution of SARS-CoV-1, the virus that caused the 2002-2003 SARS epidemic.

#### Data

SARS-CoV-1 sequence data from humans, civets, raccoon dogs, and ferret badgers were downloaded from NCBI. Metadata (metadata.csv) was scraped from primary publications and cross-checked when possible. Certain sequences (exclude.csv) were removed due to poor quality, duplicates, and because they had unknown sources (e.g., extensive tissue culture passage, lab constructs, etc). Final sequences were quality checked and indels correct as necessary (fix.csv).

Alignments were created using MAFFT, found free of recombination using GARD, and trees were built using RAxML (no bootstraps)

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**Andersen Lab**  

The Scripps Research Institute  

La Jolla, CA, USA  

[data@andersen-lab.com](mailto:data@andersen-lab.com)