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README.md

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 # Experimental reproduction of viral replication and disease in dairy calves and lactating cows inoculated with highly pathogenic avian influenza H5N1 clade 2.3.4.4b 
 
 This repository will host scripts and describe how to reproduce the computational analysis in:
-*Baker, et al. **Experimental reproduction of viral replication and disease in dairy calves and lactating cows inoculated with highly pathogenic avian influenza H5N1 clade 2.3.4.4b **. https://www.biorxiv.org/content/10.1101/2024.07.12.603337v1*
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+*Baker, et al. **Experimental reproduction of viral replication and disease in dairy calves and lactating cows inoculated with highly pathogenic avian influenza H5N1 clade 2.3.4.4b**. https://www.biorxiv.org/content/10.1101/2024.07.12.603337v1*
 
 This project is in active development. The paper is a preprint and has not been peer reviewed. 
 
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 See the respective README.txt files within the folders for details/instructions.
 - [ML_Trees](ML_Trees/): Input and output from the genetic sequence analysis: includes PDF tree figures.
 - [SNV_results](SNV_results/): Variant calling analysis. All tables and data generated from within-host variant calling analysis.
-- [Supplemental-Tables-XX.xlsx]: all supplemental tables and data associated with manuscript.
+- [Supplemental-Tables-XX.xlsx](): all supplemental tables and data associated with manuscript.