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Update 2.2.2_Viral_Taxonomy_and_Phylogeny_II.md
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vmkhot authored Sep 24, 2024
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Expand Up @@ -153,16 +153,16 @@ One of the advantages of running geNomad is that it also outputs functional anno
> 3. What percentage of your viruses were classified by each tool?
> 4. How can you judge the accuracy of your taxonomic classifications?
> 5. How many classifications agree/disagree?
> 6. Which viruses are closely related? Which are not?
> 7. What is the maximum taxonomic distance between viruses that are still connected in this graph?
> 8. What are the limitations of using these tools?
>
> **Pick one of the viral contigs annotated by vConTACT3**
>
>{:start='9'}
> 9. How many genes are shared with known reference viruses?
> 10. Which genes are shared with the other known viruses?
> 11. Visualize your virus on the network. [see homework exercises here](https://mgxlab.github.io/Viromics2024/2.2.3_visualizing_taxonomy/index.html).
>{:start='8'}
> 8. How many genes are shared with known reference viruses?
> 9. Which genes are shared with the other known viruses?
> 10. Visualize your virus on the network. [see homework exercises here](https://mgxlab.github.io/Viromics2024/2.2.3_visualizing_taxonomy/index.html).
> 11. Which viruses are closely related? Which are not?
> {: .source}
{: .challenge}
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