BME356 Functional Genomics- Phylogenetic Network Analysis

Task

Questions

1. Using sequence alignment, compare the protein sequences of the HIV-1 and HIV-2 genome with that of the SIV genomes. Suggest the likely zoonotic transfer from SIV to HIV. Add Feline (FIV) to the analysis. Analyze whether the FIV virus is linked to SIV and/or HIV. Discuss your answer.
 
2. Critically evaluate the analysis made in ‘Phylogenetic network analysis of SARS-CoV-2 genomes’
https://doi.org/10.1073/pnas.2004999117 with reference to the letters and responses associated with the findings. Discuss the following.
(a) Weaknesses (including assumptions of the underlying analysis and provide previous examples with academic references).
(b) Dangers of interpretations of such analysis.
(c) Provide facts that debunk the findings of the article.
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